Yeah i have noticed the same problem aswell, mostly with one of the human hulls, it doesnt make a big difference unless your adding big parts then it sticks out big time. To fix this problem i've just added my parts to different hardpoints that seem to work. Like i said one of the human hulls, its not the one that looks like that ship from startrek, and its not the one thats on the box its that other weird looking one that i cannot get anything to line up right at all, perhaps there is a way to place hardpoints yourself? for example, start with no hardpoints on your hull and add a hardpoint add on, meh i guess we'll just have to deal with it eh.

Most drengin hulls are also off - by a LOT - becomes notable when you use Kyro's mod and use whatever drengin hull as jewelry: The main hardpoint is to one side (and several hardpoints on other hulls are a bit conflictive as well)