You don't have to setup up UVs manually if you want to use BakedLightmaps. Godot generates the UVs for lightmaps automatically on import (there is a setting in the import tab). They are called UV2 and exist seperated from the normal UVs you create in Blender.
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That's good to know! I didn't realize Godot would generate UVs. I assumed that the UV2 slot would just be a copy of the regular UVs, which in my case would probably be too compressed to have good looking light maps.
The other concern I had is that all of the assets in my game, minus the enemies and some glass, all use the exact same SpatialMaterial. I wasn't sure if that would cause an issue either.
I'll give this a try next time I have the chance! Thank you. :)