Thank you Harpo and Norbert, I think that answers my question.
So, just to use a separate example to be sure I understand:
2 mods (A & B ), both alter the TEC Battleship (I haven't taken the time to look up the actual file name right now, sorry). A mods the ship's hull HPs, while B mods the ship's shield HPs.
In the mod manager in game, Mod A is selected first, then Mod B, which means Mod B has a higher order of precedence and will be the first one the game looks at for files.
As such, and based on what you guys just told me, this means that with both mods loaded as described above, this means that in game I'd see the change to the Ship's shields, but not the hull?
If that's the case, that kind of sucks.