Turns out we can (and probably should) hide these messages via a config file in /etc/systemcheck.d/. Something like this would suppress all systemcheck non-actionable messages (for SD users):

systemcheck_skip_functions+=" check_apt_repository"   # Skip info about enabled derivative repository
systemcheck_skip_functions+=" check_operating_system" # Skip OS updates check (already ensured in SD updater)
systemcheck_skip_functions+=" donate"

One thing to consider, though, is that because we're installing it in whonix-gateway-17, sys-whonix may end up also being affected.

Somehow I came across a double-popup. Not sure how to reproduce / what caused it, though.

Found another instance where it only mentions the derivative repository, but not donate button and the update check. And this time it showed as the system booted up for the first time and not when doing the sys-whonix configuartion step.

For the time being I've been able find a way to suppress these messages without needing to remove the dialogs in QA, but it waits ~300s trying to dismiss a potential prompt which may choose not to pop up.