Well, because PvK wants that way !
Technically speaking, it is because better engines do not provide bonus movements but give extra "movement points". They all add up and then diveded by hull's engines/per move number. It is very big for colony ship so the resulting number is rounding up back to 2 rather then 3 even for advanced engines. If you want to mod proportions in a way that better engines help colony ship, edit data data files and decrease max. number of engines and engines per move for colony ship hull. Personally, I would like it too. Itjust does not make sense that even most advanced engines can not push CS any faster then ancient ion engines I ! It is just like putting B-29 propellers on B-747 and expecting it to fly the same 500 mph !