I would imagine once policy is changed based on commander's intent (SECDEF by direction of POTUS) it becomes a zoo to have to change all the downstream military personnel policy to reflect that, but I think you raise a good question, and I don't know.
To piggyback on your question, I wonder how much of the executive/senate 'responsibility' is just rubber-stamped by staff underlings when the DoD sends them (if they send the executive/senate this info, at all) info that says 'hey, we are changing the way we promote officers, here's the info.' I mean, do they really care? I don't know.
I remember when I was promoted and saw the list come out, all the names on the dozens of pages of promotions in each and every community both active and reserve. I thought, they aren't really scouring for my name and looking at my bona vides.
Now you're making me think. Dammit.
Back when the mass firings of federal employees began, the DoD was within a day or two of the same before the brakes were pumped over the US Code. You can't go out and RIF folks from the DoD without doing a study on the effects of those cuts. I'm pretty sure the study was kind of pencil-whipped, but whatever.
Anyway, that brought to mind my question(s) and I'm not saying changes shouldn't happen (the same with the cuts) are there laws in place which have to be followed or can the SECDEF wave a magic wand and set whatever qualifications he wants? I don't know.