TFS is merely a database (albeit an intelligent one). It doesn't care what your file formats are. I think it just loads your file as an object into the database. We have used TFS for years with no issues. I have stored scripts and mxd's in TFS. I've never used it with FGDB because we use SDE. And we have tried to store entire SDE database scripts, but found it much more trouble than it was worth. Incremental database backups work just as well.
If you are a Microsoft shop, TFS is Microsoft and it plays nicely with everything Microsoft.
Good Luck
Brent Hoskisson