Can SE be prevented from using the cracked mud texture on beaches?
I wish that in general, SE could make a distinction between deserts, beaches and riverbanks. Applying the beach/desert texture doesn't have to depend solely on elevation: in non-desert areas, there could be rocks or vegetation going right up to the shoreline.
Does the new version create a places-user.cfg at some point?
Yes, it should. Have you tried repairing permissions for the SpaceEngine/config directory?