Hello Nick,
Yes -- it's actually been discussed extensively quite a few times before, especially around the time that v4.0.0 was first released. Hauptwerk v3 effectively used to work like that (with MIDI settings defined globally, then mapped to each sample set), but so many people found it difficult to understand and use, and there are so many differences between different styles of organs (and different ways that different sample set developers designated 'role codes' for different keyboards/stops/pedals/controls/functions/etc. on their sample sets), that in practice we decided that it was best and simplest for the vast majority of users simply to make the MIDI settings organ-specific. The intention was, and is, that auto-detection should make that quick and easy (although I do appreciate that the logistic issue with travelling back and forth between your console and computer makes that awkward in your specific case).
We don't want to change that design fundamentally (at least in the near/medium-term), I'm afraid -- sorry.
If moving the computer closer to your console isn't a possibility for you, then I'd recommend using some kind of remote desktop software (e.g. from a laptop or tablet), so that you could operate your Hauptwerk computer remotely from the organ console when needed.