I ran into one example of the problem with having two sets of components with the same family numbers. When I created my fighter engines, I copied/pasted from the ship components and modified size, cost, etc. I kept same family numbers, though. When I upgraded one of my ship designs, my Fusion Drive III Engines (25kt) suddenly became Small Fusion Engines (2kt). Not the worst problem you could have, admittedly.

Not only will the AI take the best component; the upgrade will take the
Last component in the file--regardless of vehicle type restrictions, etc. The only way around this is to add "foo" and "bar" racial traits, but this has two problems. 1) It restricts your tech tree to more or less the original setup, without the luxury of renaming it; and 2) it's still incompatible with TDM-Modpack et al--you have to generate new EMP files for each race in Foobar Mod. Sorry they aren't compatible; I'll have AI as soon as I find time to work on them--although someone else (who?) did mention they would be willing to help with that.
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"The Unpronounceable" Krsqk
Basic Tech Mod
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Basic Tech Mod v.75
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The Unpronounceable Krsqk
"Well, sir, at the moment my left processor doesn't know what my right is doing." -
Freefall