It's just retroactive.
The klingons' make-up was retroactive after TMP, it stopped being retroactive (by necessity) when DS9 wanted to do a Digital Forest Gump on a classic TOS story to highlight their 100th episode. Worf provided the perfect non-explanation and it was brilliant.
The Augments story arc, which I often refer to with derision as the
Ruffles Have Ridges arc, has always been for me a pointless fan-service exercise in Couldn't Leave Well-Enough Alone. With only the fourth episode of the five-part dual story actually being good, not counting the cleverly disastrous stand-off crisis at the Cold Station in episode two. The whole arc exists for the seeming purpose of building up to the klingon "explanation"/reveal, and I personally just find the whole thing redundant and fan-servicy.
With STD I like to just assume things are once again retroactive, and that we can just leave the whole Augments thing behind us. The producers can prove me wrong at any time, but I have faith they're mostly of a similar mind.
And anyway classic TOS is full of stories that never got referenced again by any other version of Trek, just because their premises were too silly or weird (galactic barriers, identical planets and "gravity assist" time travel for example). My favorite ST movie
The Voyage Home is among them. To me it is normal that every version of ST should clean house, so to speak.
I've also always regarded the production design changes in TMP, the 2009 film and now STD to be retroactive. Even when TOS "homage" episodes of TNG and DS9 implied (tounge-in-cheek, let's not forget) that they weren't.
Creatively speaking, every ST is its own universe. It can't not be when the "primary" source material is 50-plus years old.