The IV/, V/, and viio/ settings should be usable together with the borrowed chord option, so that constructions like IV/♭III - V/♭III - ♭III (in Major) and V/IV - V/VII - VII (in Minor) are possible.
I am fairly sure Hookpad is capable of this already. Please add these in Hookpad or Hookpad 2 (along with other types of applied chords while you are at it).