I'm starting to have to question why you have to go through this entire rigmarole in the first place. Your Z alignment in the stockholders should not be off at all, but you are correct that the cad system does dictate the orientation of all of the parts in the implant Library. This is not a bug this is on purpose, the cad has to know the alignment of all of the parts in order to create a correct design, if any of these parts are misaligned then the design will be off by a large margin. The cam does not have to know all of the parts in the system however it does need to know the important part in this case the abutment. If you were in the business of manufacturing your own titanium base then the important part would be the titanium base. If you were in the business of manufacturing the implant then the implant would be the important part. The fact that you need to do realignment of any of these pieces causes me to be concerned that something was overwritten in your previous installation or should I say your newest installation of your cam. This alignment of all of this pieces should never need to be touched the fact that you need to do it is worrying. I do not think that your cam supplier support would simply shrug you off as though there were no problems. If you have explained to them all of the things you have done to try to find the reason for the long time, and this misalignment, most cam providers would easily create a new installation because as above it should not be something you need to modify. Yes the cad and the cam do need to talk to each other but only in so far as the important piece to be manufactured. Other data pertaining to the case need not be communicated. How did you arrive at the conclusion that your surface was 0.58 mm stretched in the wrong direction? Did you manufacture something ordinary such as a cube in order to determine incorrect sizing? Did you fire your last machine operator?
No the cat does not take into account any of the cam surfaces. CAD operations must occur before cam and not after. So the cad will not use any cam surfaces in order to generate CAD data.