Have you ever been there? Getting into ES2 for a few game, and you love it, and want to mess around using custom faction to see what whacky combination you can get out. 

In particular, I've found that Shipbound and Riftborn population producing mechanics are interestingly OP together (However, the population production price is quite low - the same price as a normal population for normal Riftborn - so pair this with some kind of nerf - like Immaterial Population, so you have to use the Riftborn's manpower production for most of your manpower needs - to balance out), as opposed to plain OP combinations that remove gameplay (like Genehunter + Extreme Foremen + Planetmender + Sowa starter minor pop). 

But then here is an obvious problem: by choosing Riftborn affinity for its population production trait, you are also locked with the Riftborn ship choice and quest lines. While the Riftborn quest line does have strong interaction with the pop prod. trait, the ships do not at all. :/

Alternatively, if you like the Riftborn "lopsided, vulgar display of raw firepower" ship design, you are now locked with the pop prod. trait. Which does not make much sense to me. 

There are key gameplay elements that can be shoved into custom traits instead of affinities, like settling with Agrosy, or using Portal (with mod only, but works fine), so I think Riftborn's Pop production trait can definitely be separated. One of, if not the biggest difficulty I can think of would be quest interactions (already buggy + Riftborn has 1 quest that benefits the pop production specifically), but I think it will be fine with some quest modifications - like other affinity would when detached from some of their key traits.