The only thing different is what shows up in the info boxes (as noted in the first post, TMO includes info for after the war. Mine is comtemporary to the game time frame), and maybe the 50 cal. I don't remember if TMO enables it or not, but if it does, the difference there would likely be the ammo loadout for it.
One other difference might be if TMO changes the availability dates from stock.
You can take those parts out if you don't want it to overwrite the TMO files. That'll just leave you with the office links part, one of which is actually from TMO.