I assume they won’t be dismantling the medium to build the large? Just doing a custom build to the same spec as the one already in the shop, but with a large frame.
As to them adding the build cost or not. For the medium they’ve built it up as a marketing piece, to earn them money (you’ve seen it an wanted a large, others may have seen it and wanted a small etc) so the profit they get from those builds is used to offset the time and cost they sucked up to build the medium in the first place.
Also assuming the ‘bike’ is only available as a frame only, so by having a custom build done to a spec someone has already dictated seems a bit of a wasted opportunity, especially if there is a build cost. You say they’ve gone above and beyond in the past, setting up accounts just to get stuff you want. Do you not feel this is a service worth paying for?