There is no scenario in which the designers should not be paying very close attention to "how the game is actually played, even when it's different from the rules". At the very least, that should inform the next edition significantly. It may inform design decisions within an edition, too. We're not talking about "one table" or something. We're talking almost certainly well over half of groups (I would say) largely ignoring VSM. If even 10% of tables are reliably ignoring a bit of the rules, they should be considering why that's happening.
Unfortunately this is a great example against your point.
The encounter guidelines are the result of very peculiar and counter-intuitive design, and we know that a large number of groups do not closely follow them (somewhere between 20-50%, I would guess, perhaps higher if we eliminate groups using pre-gen adventures only, because they're not responsible for their own encounter design, if they're not following them, that's on an author somewhere), in large part because 6-8 resource-burning encounters every single day is just not a good match for most of adventures people write, and stories people want to tell, with D&D.
And before you suggest all the people new to 5E religiously follow them or something, all the evidence we have available is that people new to 5E have a lot of difficult with the 6-8 encounters/day concept. They don't instinctively follow it, it doesn't make sense to them, and they end up on messageboards going "Why are my encounters so easy!?!" and so on. And I'm a human, and I have a fairly good idea how humans think, and I know this is not something that is going to "click" with people in the way experience or initiative does. The figures are only going to be lower for that group than the more serious players.
WotC absolutely should be paying extremely close attention to this. Even it's 20%, that's significant, and I suspect it's much, much higher, maybe even a majority. And what should be telling them is they can't design D&D to require 6-8 encounters/day. That's mental. They need to either just dial it back, to say 3-6 by default, or work out a way to have a more flexible system in future.
They do need to be consistent, of course. All current subclasses are designed on the basis of 6-8 encounters/day. So future ones should be too. But for the future of D&D, they need to find a different path, whether that's 5.5, or 6E or whatever.