Do tiers spawned with the built in command obay the same mod settings like the tiers native to this mod, or will I have to add my own mod settings to compensate?

The base mod's settings will apply to all tiers that are created via the API, so you should be good to go without extra customization if you're looking to match the vanilla tiers.

I'm getting complaints that my mod may be messing up auto rotation. Does overriding the entity collision masks do that?

Namely, my space loader doesn't snap to belts.

Changing the collision masks shouldn't mess with that.. hmm. I'll dig into this.

With the help of someone on discord, I found the likely issue.
It seems like your mod is using the order field to mark its own loaders, and me modifying that mucked that up. I'll see if adding back the suffix fixes it and report back.

Regardless of the result, you should probably add that to the documentation.