Not sure what you mean by reverse-engineered, Tom. I think that the 2D CPs are projected according to the active alignment. If the alignment is slightly wrong, this leads to certain reprojection errors of the (hopefully correctly placed) Control Points. Ideally, with a new alignment RC is convinced our CPs are right and hence the errors smaller.
BTW, it is absolutely possible to get CPs with 0.0 px error. It’s a matter of practice and a bit luck… 