Setting admin theme using Profiler
One way to accomplish this is to use Strongarm to set the admin theme variable as part of a Feature. 

Given that the "Standard" Drupal installation profile creates a lot of other stuff that won't be in a custom installation profile -- Basic Page and Article content types, for instance -- I've created a Feature with all those and added the Admin Theme Strongarm variable as part of that.

That said, leaving question open in case somebody knows how to set the Admin theme as part of a Profiler makefile.