This .cfg works indeed, the problem seems to be about not starting life support and habitation on the SSPXR.
The following picture shows two exact copies of a craft, the lower craft (in the ls-tab) is a craft that was launched long ago, with a fresh cycle of kerbals.
Their hab timer matches the hab timer of the newly launched, identical craft that has not yet started its life support and habitation.
The following image is of the hab timer after replacing the standard .cfg with your .cfg.
After using your .cfg I could actually activate the hab and life support on the SSPXR modules.
The MB2 tabs on the hab modules now have both a start habitat and stop habitat button after starting the habitats, normally there is only one button, that changes to the opposite of whatever state the module is in.
Also, here's my KSP.log: https://drive.google.com/open?id=10pExI0Wa1JeQMpfelBQ86GnorUb4QA9j
EDIT: I found more problems: The hab timer doesn't actually seem to go down for either kerbal, or only one kerbal at a time. EVA-ing and boarding resets both hab timers.