A centerline established prior to glue up isn't absolute either. As you noted, it can be less than perfect coming off the form.
I find centerlines unneeded until after glue-up, and since they can't be perfectly trusted following glue-up.... I draw them on there afterwards. To do so, I put the bow in the vise so it's level side to side, run a string weighted on its ends, from one end of the bow to the other, orienting it so that it bisects the bow blank down the middle of the riser and limbs as much as possible. Then mark it on the ends where the string sits, and drop plumb lines down from the string to the bow in a few places on each limb and mark them there. Remove the string and connect the dots with a flexible straightedge. That's your centerline.
If you DID put a centerline in your glass prior to glue up, say, in a one piece bow, this method can be used to verify its accuracy after glue-up. This method can also be used for layout/alignment of centerlines on takedowns following drilling but prior to shaping limbs.