Hi Xori!
Have been playing X-mod lately with MSI2 and thought I should post some of my thoughts on it so far. I added a ton more mods (some add minor functionalities, others are QoL), do let me know if you'd like the full mod list. I've been testing balance with all these.
Though overall, I'm loving the logistics challenges from X-mod combined with combat challenges from MSI2! Will post a full synopsis once I finish the playthrough as well.

Thanks for making X-mod!

Current state: 16 hrs - Chemical science

Things of note:
1. Initially tried with X-Mod + Rampant (instead of MSI2) but it became very difficult with just the pistol - maybe will reattempt it after this run.
2. Also tested balance with Warehousing mod but those have very high capacity making the challenge of low stack sizes and compression obsolete. Or maybe not as the challenge is moving materials and not buffers, removed the mod regardless.
3. Clearing first island was easy with David in early game. Effecively removing the biter threat from MSI2 missions altogether.
4. Eventually added Noxy's Swimming mod in the mix too, so biters can swim very slowly and attack your ships - but then you can swim too though very slowly. Realized I needed it anyways due to missions spawning in deep water or smaller surrounding islands. Biters migrating across water to your island also seemed interesting (need for defences around shores). I does kinda break the balance somewhat (once spiderling is unlocked - still a bit split on this decision.
5. Needed to transport Titanium from far away, which turned out to be a major eye opener as the game opened up around trains. Setting up logistics of sending wooden boxes and getting compressed Ti in the same train was super interesting! Still figuring out how to standardize train schedules (can't just go "empty train inventory" at requester stops as need to send back the empty wooden chests too). Will experiment more.
6. Been a hot minute since I played vanilla but was missing AAI industries a lot. Mostly the recycling. Stone furnies, wooden poles, etc. kept piling up in chests of shame.
7. Haven't unlocked it yet, but wished for spiderling to be available earlier than requester chests, as I believe it'll be more difficult to set up and scale compared to a logistic network. Also, not sure yet how swimming will break balance for spidertrons, might have to disable it to keep spidertrons local to their islands.
8. I also mostly like to play green and was looking for a mod to add that can help with pollution (like air filtration etc.) because pollution doesn't really go well with island maps. But haven't found any that is not a total coal sink (since getting and transporting resources is already a big challenge). Still figuring this one out...

Some issues encountered:
1. MSI2 Oil mission spawns on deep water but needs David to be close to it. Couldn't be completed without spawning in deep landfill via editor. Realized later I could've added Noxy's Swimming mod earlier instead.
2. Don't understand the idea behind fuse poles - they're more costly and more likely to explode. They unlock early game but don't know why I would use them. Maybe a T&T entry or Tech description? Maybe they need to be cheaper?
3. Different pole types don't spawn wires between them automatically, which is good I believe but not explained properly, maybe a T&T entry or Tech description?
4. Ironclad has better health, attached gun, more storage (20) vs Boat (from Cargo ships) has less health, no defence, and less storage (15) but faster speed. Boat also completely gets superseded by Hovercraft once you unlock that. Could be balanced somewhat?
5. "Stack size tooltip" mod reports stack sizes incorrectly but debug tooltips are correct. Weird.
6. An escort mission from MSI2 spawned on a nearby small island rather than the mainland, which, well effectively rendered the game unplayable. Added Noxys Swimming mod to get past this issue.
7. Underground pipes tech is placed after blue but takes only red and green science. Mostly because of Titanium dependency. Felt weird, and was a bit inconvenient without those, but worked out just fine once I unlocked them later.

Thanks for the feedback!

2 Also tested balance with Warehousing mod but those have very high capacity making the challenge of low stack sizes and compression obsolete. Or maybe not as the challenge is moving materials and not buffers, removed the mod regardless.

Warehouses shouldn't be a significant balance concern. It is the transport vehicle inventories that have heavy size nerfs for balance, the container inventory sizes are only halved by X-Logistics. Basically inventories holding intermediate (i.e. crateable) materials need the divide-by-10 change, which are trains/ships. Containers/warehouses are just as likely to be used for non-crateable materials so I don't want to heavily nerf them.

3 Clearing first island was easy with David in early game. Effecively removing the biter threat from MSI2 missions altogether.

I didn't really consider biter balance much when creating the new map gen. Obviously having islands will always help against biters, but maybe there's scope to increase their default settings a bit.

6 Been a hot minute since I played vanilla but was missing AAI industries a lot. Mostly the recycling. Stone furnies, wooden poles, etc. kept piling up in chests of shame.

I won't be adding arbitrary overhaul support in X-Logistics but I'd like to do K2 and AAI Industries. They probably wouldn't work with Sand & Glass and Nuclear Fuel though.

7 Haven't unlocked it yet, but wished for spiderling to be available earlier than requester chests, as I believe it'll be more difficult to set up and scale compared to a logistic network.

Spiderling should be a blue/chemical science unlock. Perhaps you've got another mod changing that?

Also, not sure yet how swimming will break balance for spidertrons, might have to disable it to keep spidertrons local to their islands.

Indeed, having automated spidertron patrols over water certainly isn't part of the intended balance. Could be fun though?

8 I also mostly like to play green and was looking for a mod to add that can help with pollution (like air filtration etc.) because pollution doesn't really go well with island maps. But haven't found any that is not a total coal sink (since getting and transporting resources is already a big challenge). Still figuring this one out...

Let me know if you find something :)

2 Don't understand the idea behind fuse poles - they're more costly and more likely to explode. They unlock early game but don't know why I would use them. Maybe a T&T entry or Tech description? Maybe they need to be cheaper?

Fuses are for placing at the entrance to your subnetworks to protect all the poles in it. They are definitely optional, you can get along fine without them if you're careful. I'm happy to consider some better balance for them though, and adding some T&T is on my to-do list. https://mods.factorio.com/mod/PowerOverload/discussion/601c29609250294d7c9b3600

3 Different pole types don't spawn wires between them automatically, which is good I believe but not explained properly, maybe a T&T entry or Tech description?

It is in the mod description for Power Overload, but yes, something ingame would be good.

4 Ironclad has better health, attached gun, more storage (20) vs Boat (from Cargo ships) has less health, no defence, and less storage (15) but faster speed. Boat also completely gets superseded by Hovercraft once you unlock that. Could be balanced somewhat?

Good points, but definitely not a priority.

1 MSI2 Oil mission spawns on deep water but needs David to be close to it. Couldn't be completed without spawning in deep landfill via editor. Realized later I could've added Noxy's Swimming mod earlier instead.
6 An escort mission from MSI2 spawned on a nearby small island rather than the mainland, which, well effectively rendered the game unplayable. Added Noxys Swimming mod to get past this issue.

I think Noxys Swimming is just going to be a requirement for MSI2 compatibility tbh. I can't predict every mission and I don't want to alter the balance just to fit with MSI2, particularly as I've never played it (although reading your post is making me want to play it!).

5 "Stack size tooltip" mod reports stack sizes incorrectly but debug tooltips are correct. Weird.
7 Underground pipes tech is placed after blue but takes only red and green science. Mostly because of Titanium dependency. Felt weird, and was a bit inconvenient without those, but worked out just fine once I unlocked them later.

Will investigate.