Does not recognize any mini machine as an entity to upgrade, manually replacing will clear the settings of the machine your replacing

Ahh, I tested this and it was working before, but one of the last few changes I made was to mark the new entity as "hidden", which apparently prevents it from being upgraded by planner. Marking as "hidden_in_factoriopedia" seems to work properly while keeping the menus clean, so that works well enough!

Fixed in v9.4.2

So, yes upgrade planner now correctly flags it, but when it actually upgrades even manually with a mini version, it superimposes the normal size OVER the mini, the mini still exist and remains working under it, somehow? lol

Hmm, you might need to detail me your process, because using the upgrade planner on mini assemblers completed normally and successfully for me with both construction bots and space platforms.

EDIT: Oh, you can't actually upgrade-in-place manually, using items from your inventory, so I'm not sure what you mean by that

Another mod was auto placing as I tried to upgrade, disabling it I see that it uses the planner to mark it, robot works, it appears to be https://mods.factorio.com/mod/autobuild specifically causing the weirdness

Hmm, just giving a glance at the code, and it seems to be checking what item is needed to place the ghost (i.e. the one being used by the bots and space platforms, the full-sized mini machine) and then haphazardly places it on top of the original, without checking if it's a valid spot for construction.

I believe this would be a bug on their side (although I probably need to update the control code on my end as well, to allow manual upgrades to begin with, just a minor oversight on my end)

I can offer you Picker Extended, which has similar ghost revival functionality, but doesn't just auto-build things in a radius around you; it requires you to be holding the item in the cursor, then mouse over the ghost entity.

It's not as free as Autobuild, but I tested that it works with upgrading mini machines, and it still saves you clicks, by allowing you to just mouse over a bunch of entities and upgrade them all in one swift movement.

EDIT: Updated to allow for in-place upgrades of resized machines (so holding a ghost mini assembler t2 and placing on top of a mini assembler t1). It might require two left-clicks (one to mark it for upgrade, one more to actually place)