About as well as installing any major total conversion over another conversion. In other words, not so well.
Why wouldn't it? The 2 mods are playing with different sections of the game. The only overlap is with the ships, so if you made sure this was installed after KM:R, any conflicts wouldn't stop either working.
It's quite early in the development of either mod to know for sure. It would be nice if you guys would work together to create one amazing mod, but right now it's two different projects. You are forgetting hardpoints, balance, and multitudes of other factors that probably have not even been thought of yet.
So it might happen, it might not. It would definitely be possible after both are released for someone to integrate them.