Well, the executable can have a version number consistent with the splash screen - surely that's within the governance of compilation / linking / building.
I don't know how the patches originate, but I suspect they come from Stygian and GOG just wraps them in their own GUI widgets. (I doubt that Stygian only provides GOG with a full installer for each subversion, and GOG generates their own binary diff.) If indeed Stygian produces the patch, it can simply contain the new version of all the resources modified since v1.0.0.0. When it is run, it can therefore update a v1.0.0.0 installation or a v1.0.0.1 installation or a v1.0.0.2 installation or a v1.0.0.3 installation or a v1.0.0.4 installation or a v1.0.0.5 installation or a v1.0.0.6 installation to v1.0.0.7 simply by injecting the v1.0.0.7 resources it contains. Stygian hand this patch over to GOG, and GOG wrap it in their GUI, and the one patcher is then useful to all players regardless of which old version they currently have installed.
Anyway, it's just a suggestion for an ongoing approach to take to patching.
I'm just as happy if the full patch is available for download the traditional way from underrail.com - as long as it's a patch that can bring multiple origin versions up to date.