The problem is, with a TTRPG there will always be people who use the game outside of the parameters.
You are correct that there are always groups that play the game so different from the defined norm that the system cannot account for it.
So then the critique of the game resolves around how wide are those parameters, and how sensitive is the system to change.
Let me take a look at my last party for an example:
7th level party: Rogue (thief), Fighter (Champion), Bard (Lore), Artificer (Alchemist), Warlock (Book), Barbarian (magic one, its the UA one that had wild magic effects can't think of the name).
Most of the party had a feat (and none of the big nasty ones like GWM I generally houseruled those out), and generally 1 magic item, +1 magic item for the group as a whole. Most items were uncommon with 1-2 rares. No multi-classing
So is my party insane, nuts....completely outside of the sandbox? I have 6 players (which the system does account for, so this is "standard" for the model). I am using a few feats and a few magic items, so clearly my group is a stronger than the baseline, but is this really the party that the designers looked at and went "no sorry that just destroys our mold, DMs really should not allow groups like this"
Because that's what it feels like when my players routinely face Deadly x2 fights and come out fine. Once in a while, sure there was a special synergy, someone got surprise, my players used a cool trick, etc. Curbstombing a fight unexpectedly is not the side of a broken system. But fight after fight after, when I start using deadly x1 as my "easy", and deadly x2 is my "medium".... something seems wildly off.
Now again, maybe it was just that party. Maybe they were just insanely synergized in a way I had not expected, so maybe that campaign was the odd duck. Except....it happened in another campaign I ran. Completely different party, and yet same things happened. And then.... it happened a 3rd time. When 3 campaigns go by and I found "deadly x1" to be the bare minimum I would even run an encounter....then yeah something really seems off.
Now was the CR system in 3e perfect? Hell no. But it was just as simple as 5e's system if not more so, I ran many campaigns in 3e and 3.5..... and never had this problem. Did I have to make some tweaks to account for a specific party, sure, of course, as any good DM must. But they were tweaks, I didn't toss the core math out the window and basically double the difficulty of every encounter just to get some challenge for my players (and 3e had WAY WAY WAY more options than 5e does). The fact that I am constantly having to do that for 5e tells me that something is off there. That is the table experience that I have generated.