The problemi snot how many mods can be run at a time - you can theoretically merge any number of mods - the engine doesnt care how many changes you have made as long as they are stable.

The problem is compatibility. You ask why rebalance contains ships, my first answer would be why the hell not? Seriously tho as a simple example Rebalance changes the engine speeds of all the ships, this is clearly a balance issue so is fair enough. If someone was then to design a ship they would need to know what the stats for all the engines are so they would know what one to put on their ship, or what speed was average so they could do their own engine. Even if they did this their ship would then fit rebalance but might be totally out of place in another mod. This is obviously a simple example, when you start adding bases, systems new missions etc. it becomes far more complex.

A modular (geddit?) mod system would be nice, but i doubt it would ever be practical, better leaving it to the 'blue chip' mod makers to absorb good ideas and adapt them to fit.