no matter what type of manufacturing and fabrication you are talking about, the end result is never exactly as designed, there is a tolerance involved, unless of course you want to pay an exorbitant amount to use only the ones that are exactly as designed and throw away the other 94%.

the reason you supply 1:1 of the soldermask is that each fabricator has different equipment and processes than the next
they will "grow" the data such that you will not have solder mask on your smd pads, and 1 mil max overlap on your thru hole lands

they have to allow for mis-registration between the solder mask pattern and the lands, you can figure out what this mis-registration is by looking at their technology roadmap, typically, the tighter the tolerance, the more you pay because the equipment to do it is newer and more expensive (if you have very fine pitch devices, there is no choice but to use it)

if you always use the same fabricator (such as in-house fabrication) then they may want you to adjust the s/m pad sizes up front, but to do so without this requirement is to bring pain onto yourself, your fabricator, and nearly everyone else involved

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