I propose that, rather than stacking multiple zones in the same place, individual zones be allowed to be used for multiple purposes (or even no purpose at all). This would be accomplished in the zone interface by making the list of zone types be a set of non-exclusive options that can be checked or unchecked individually.
In particular, the ability to have a “nothing” zone would allow hospitals to be set up in the new version without them becoming overcrowded with dwarves that are just hanging out.
Primary, Secondary, and Tertiary zones might be a good method to explaining it.
Like you say, you could set the primary, discreetly just a plain meeting zone in a large square around the interior. Then the secondary hospital ontop of it and outstretching outside of the primary zone to additional rooms, with a temple in the far side of the shared hospital on a third tertiary layer, (furniture assigned to the 'highest' layer at a time) with the painting controls working like the priority levels for seeing and interacting with a layer at a time.
This could be used for things like memorial halls, which would be a tomb over a meeting zone, and would automatically start 2nd/3rd layer painting when interacted with ((memorial halls are absent from 50.04 because furniture room painting is disabled))