After some kerfuffle on a bug report[1], it was made clear[2] that using "make config-conditional" for a port which involves FLAVORS (such as any Python port, and many others) is not supported.
I must confess that it does not make sense to me, but they were at least clear on that point.
Portmaster, internally, uses config-conditional, so I guess this is something that should be changed.
To retain the current behavior ("only show config dialog if there is a new option the user has not configured already"), I guess portmaster would need to save this information separately, somehow? I know the whole point of portmaster is to rely on the ports system to do the real work, so I'm not sure how best to square these two competing forces.
[1] https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=286659
[2] https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=286659#c18