This would be difficult to make happen in practice. This may make sense to implement for the active component and maybe retirees, but would likely screw reservists and veterans. If you want to give COLA to the latter two parties, you'll likely not realise the cost savings and end up with unintended consequences (i.e. fraud).
I'm puzzled, because as a SELRES for going on 6 years, and an AC person for 10.5 years prior to that, the commissary was a "nice-to-have," but what does it really get people that you can't get at a Wal-Mart Supercenter?
I can't think of the last time I actually went to a commissary for something I really needed that I could only get there. I hit up Bragg's occasionally when I was MOBed, but only because it was a more convenient stop between work and home than Harris Teeter. And the Class VI (Army talk, I know) was right there, so I could get beer and/or booze. If I was really hurting, I could have (and did from time to time) slummed it and hit up the local Food Lion instead, sans beer or booze.
I can't think of any time since I left active duty that the commissary factored into my life as a reservist. And I never really shopped there while on active duty, either. I'd argue it's a dated benefit held over from when bases were a lot more isolated than they are today.
Edit: Spaetzle. German Spaetzle. As a Pennsylvania Dutch kraut, I do like my occasional sauerbraten or wurst, and Bragg's commissary helped cover part of that craving for like a year of my life, max. I could do the meat and rotkohl myself. But I have Amazon Prime for that, so why does that justify an entire bureaucracy in DoD?