So, for the moment, the level builder is an external program, which makes some aspects of it easier to debug. As I'd left off the main program for a bit to go build levels with a bit more Z interaction, I managed that relatively quickly:
The colored zone edges you're seeing as I pan up are the up-down ramps, where they are absent you're seeing more than 1 z level of separation, so essentially a cliff.
Technically I could go back to the main program and finish testing movement up Z levels, but there's still a bit of work to do with level generation, in terms of making more realistic terrain and some non-ruined cities, so that'll be next.