With any supermod, there is a short list of stuff that's safe to add
- Sub and ship skins
- keyboard layouts
- radio and gramophone mods
- alternate plotting systems
We used to say missions and campaigns, but we now know that unless those missions and campaigns were created on a machine with TMO installed, they might not be compatible.
Added ships might not be compatible, although TMO's campaign is written so that adding ships is not the game breaker that the stock game is. Especially if you play RSRDC with TMO you should NOT add ships to the roster.
Finally, there are mods designed to run with TMO. These are compatible in the sense that the game does not crash when you use them. Some, like RSRDC, are supermods in themselves which overwrite TMO settings in many areas of the game. Some, like OTC stay pretty fairly in their announced territory and leave TMO gameplay essentially unchanged. But since "compatible" means different things to different people you can't rely on the term to mean anything at all. Try 'em and see if you like 'em is the only advice there.