If the bike looks like the one below, then the further back from the rear stays the brake is the longer the drops need to be to hit the rim's braking surface. So while two sets of brakes might have the same caliper length, they can still have different reach.
A trick exists, if one wants to, mount brakes in front of the seat stays rather than behind to manipulate reach. There is no reason why it shouldn't work reasonably as long as one swaps the pads around, but there are
complications for recessed nut systems and I can also understand it if one doesn't like the look of it... The obvious alternative solution is of course to measure what the potential difference needs to be and pick brakes that cover the range.