Hmm, so you're saying that the machines are being unlocked early, but only some? I might need a modlist for that; that is an odd interaction. If the tech tree is enabled, then unless the vanilla versions were unlocked from the start, it should place the mini version in the tech tree. Or if the original technologies and unlock requirements were altered.. maybe. There's also the possibility my copy function is broken. Maybe. I've added some error checking and ensured that "enabled" status is copied. Hopefully it works in v4.1.5
As to the other mods.. I'm trying to keep this mod towards assembling machines, furnaces, and mining entities (with tanks and beacons being the exception). AAI is more a vehicle mod, isn't it? I haven't looked much into it; too much complicated circuitry for me.
As for FactorioExtended, I know even less about it, but isn't it similar to bobs mods? I could possibly try to extend support towards their machines.. although my personal preference is to bobs-angels.