There are very few things in the MDS file that would typically need to be checked in/checked out per user. Adding new project level variables, new major components (like adding the TestedApps component... not adding individual apps), and new Test Items are those few items.
While the MDS file DOES change when you add new script units and keyword tests, the MDS file does not control those. That's controlled by the Script.tcScript file and KeywordTests.tcKDT file.
So... at least for the part of what I've done in the past, having a central person in control of the MDS file is probably the best solution... gate it, make it so that a very limited number of folks actually do that process, and you'll reduce your risk.