I did get Black Magga as the villain in quest mode, with Nightbelly Boas as henchmen. Defeating Black Magga with nowhere for it to escape did not end the scenario. I was able to win by closing every location by going through cards (was very close). BM is still a villain though, so if he is defeated and can't escape that should be it.

 

Also why are we getting such a lack of diversity in quest mode locations (level 37 at the moment.)? Is that possibly working as intended?

Can 2nd this one.... At least sort off

 

I faced Black Magga but did not close all locations. Once he was defeated he did not 'run away' to a new location. Instead the card was detroyed (same visual effect). The villain/henchman reshuffling did not occur.

 

I did not manage to close all locations so not sure if i would have won.

Defeating Black Magga in quest mode doesn't close the location.  But you can still win if you close all locations after defeating it.  I'm not sure if this is intentional or not.