In the shipdesigner you currently cannot align different parts on one single axis. I tried it multible times, but each time the parts are always ofset by 0,5 degrees to either side. There is no middle axis for ship designs, so each part can't be centered perfectly. In turn this means that if you mirror a part, it is not mirrord correctly but will be ofset to one side as well.

I would like a imaginary central axis that can be used for excactly that purpose to be implemented in the ship designer.

Update: This problem only occurs if I try to align parts by using the "ofset" controls, not when placing them via hardpoints.