I have used Simulink Projects with GIT for a while and had few problems with it. The files in the resources folder should only be added or removed as you add or remove files from the project. Making changes to files already in your Simulink Project should not affect what is in the resources folder. Make sure users are looking at the resources folder to do GIT add and commit at the same time they are adding and committing other files in the Project to GIT. The use case of a file move/rename can cause odd behavior because the next user pulling the changes may have their Simulink Project looking for the old file name or saying the new file name is missing from the repo. But it is easily recoverable, they can just manualy remove the old resource file and re-add the file under the new name to their project, and commit/push.
Simulink model and data dictionary diff/merge is a different thing, always handle this with care. These are not text files and the diff/merge tools can only do so much to help understand what was changed. If there is a conflict, my preference is to first understand what the last developer did to the file and then decide whether to manually merge my change into theirs, or to manually merge their change into mine.
