Object Mapping is a property of the specific project because, from one project to another, you may have different object mapping requirements. I've seen the behavior you've described where it appears the object mapping is changing when it actually isn't. I think this is simply a matter of how the project loads on different machines and then, when you save it, that it saves the object mapping in different orders and such.
As for the conflicts for keyword tests, when you add a new file to a project (and adding a keyword test as well as a script unit does this), there's a "Files" section in the MDS file that gets updated. So, everytime you add a new item, that file gets updated.
Now, as a general rule of thumb, if no actual changes were made to specific project level items (such as test items, object mappings, project properties, "persisted" project variables, etc), when my source control app notes a difference between server copy and local copy, I usually just ignore it and overwrite. The "files" section will update next time the project loads and the object mapping, as mentioned above, is simply a matter of order.
What you may be experiencing with TFS may be a quirk of that source control system... I can't say for sure, but your MDS file scenarios are an annoyance, but one that can be easily ignored just by telling TFS to download and over-write.
