Hi,
Unfortunately, there is no simple checkbox to disable auto instance meshes, but there’s a workaround you can try.
Actors with different materials / material properties, you want to keep them separated - I believe this is the case for overrides as well; https://forums.unrealengine.com/t/issue-generating-geometry-collection-on-mesh-with-multiple-material/1617654/2
While it would take some manual labor, you would need to duplicate the static mesh assets in the content browser and assign materials there, then use them when creating the geometry collection.
Regards