Not sure if I set up something wrong but line 36 in gltf_level_importer_base.gd, i.e.:
var extras:Dictionary = state.get_additional_data(CUSTOM_DATA) as Dictionary
will throw an error if the object doesn't have any custom properties and the rest of the function doesn't execute (so materials don't get replaced, etc).
You can fix this by just setting any dummy custom property in Blender but I found this annoying so I replaced the line with:
var extras = state.get_additional_data(CUSTOM_DATA)
if extras == null or typeof(extras) != TYPE_DICTIONARY:
extras = {}
else:
extras = extras as Dictionary
I'm using Blender 4.3.2 and Godot 4.4.1 btw.