you might be right. i can think of a nasty hacks to do it. but as clean as either a centralized repo or
having the mounts twice. one with the mountpoint and another with a root setting that points to a subdirectory that holds the _modules directory.
another work around would be each team having 2 repos one for the modules one everything else. with the modules ones being at the root.
thing to consider with all of these solutions is that for each repo added to gitfs it is going to take more time to do filesystem.update
this is kind of why the centralized repo with PR's makes sense. it might be more work, but it encourages auditing. and in the end it is a better representation of what salt actually has.
as is they are going to have to avoid clobbering of the _modules directory anyway. no matter what solution you end up going with. [even if it worked perfectly all the modules sync system does is install the modules into the cache under a file system directory. so the clobbering would happen there]