This might be a bug, or not.
If one of more items to be installed is marked as an “apple_item”, Munki will not check for Apple updates, in an attempt to prevent this sort of problem.
In looking at my repo, I notice that my current InstallVentura item for Intel is marked as an apple_item, but my InstallVentura item for AppleSilicon is not.
So:
If your “OS upgrade” item _does_ have apple_item set to true, and Munki is still checking for Apple updates and MSC is prompting for them, then there is probably a bug to be addressed here around this behavior.
If your “OS upgrade” item _does not_ have apple_item set to true, add that key and value to the pkginfo and retest your scenario.
As a side-issue, the code that creates a stage_os_installer pkginfo item should probably also set apple_item to true.
-Greg