I agree with those who believe there is probably some "tolereance drift" both within a starship and across a starship's class. Since we know starships are not built as perfect copies by replicators, there is likely some variances in the tolerances of each ship owing to a whole constellation (excuse the pun) of factors. And heck, what is not to say there is not some "tolerance drift" in a replicator?
Yes, it's 300 years in the future and manufacturing techniques will no doubt improve steadily over that time, but these machines are being built partially on the ground (in a gravity well) and partially in space (in a microgravity well). Such variations could very well impart their own variations on the structures.
Now, chances are the tolerances for a structure as large as the mated surface areas of the GCS saucer and neck are tight enough to allow interchangeability of "stock" saucers (ones that were built to the same specification and as such likely have pretty tight tolerances). Anything within a couple millimeters (which strikes me as reasonable for mid-24th century tolerances) would likely be fine.
I imagine the docking clamp system itself forces the two pieces into the proper alignment as they get closer (since I doubt the ship's motion and position control system is accurate to the nanometer level), so provided the tolerances are close enough, things like EPS taps and turbolifts should all mate correctly.