Given that franchise evolution, it does seem strange to suddenly invoke Roddenberry in this context; many aspects of Star Trek as we understand it now have long since gotten away from his intentions.Original intent has become irrelevant since the franchise has evolved so that even successive productions have a fairly good idea of how far they can take their innovations in relation to what came before. It doesn’t matter what you or I think or even what Roddenberry thought; these solutions just come together as if by gravity, because the single-universe precedent is so well established.
I talked about this at considerably greater length over in the "Discovery and the Novelverse" thread, but these choices on the part of Discovery also tack against the general trend in other franchises, which (as you mentioned) currently tend to either maintain a central "gravitational core" of single-universe consistency or use an in-story multiverse to explain incompatible versions of something/someone (so that every version "really" exists).
Overseers of franchises like Lucasfilm and Marvel Studios are now formalising this effort towards such consistency (including visual consistency) by having in-house departments devoted to it--the Head of Visual Development for Marvel Studios was just interviewed on Kevin Smith's podcast this week, and he goes into a lot of detail about how important it is for them not to change previously established elements between movies/series in the MCU and how the studio regrets not establishing that more firmly sooner (so these thoughts are fresh in my mind again

As long as I'm making that analogy, nothing makes the changing trend more clear than how the span of time between the premiere of Iron Man and today is equal to the span of time between the premieres of TOS and TMP.