I was wondering if it was possible to have custom light guides, zones, and profiles on the S88 MK3?
As well as the potential compatibility of those light guides with MainStage.
Not at the moment. I think zones and MIDI templates are planned for a future release. There's a thread here from NI about the future of the MK3 and Komplete Kontrol/Kontakt integration - Kontrol 2024 outlook: what was, what now, what next? — Community (native-instruments.com)