Honestly, although it's not exactly what you are mentioning, have you read the section called "modifying encounter difficulty" ? "Increase the difficulty of the encounter by one step (from easy to medium, for example) if the characters have a drawback that their enemies don’t. Reduce the difficulty by one step if the characters have a benefit that their enemies don’t. Any additional benefit or drawback pushes the encounter one step in the appropriate direction. If the characters have both a benefit and a drawback, the two cancel each other out."
So one issue with the difficulties area, is what happens with 2x, 3x, 4x type deadly.
Does a 2x deadly drop to "just deadly" with a situational benefit, or does it drop all the way to hard?
Such a rule would not be necessary if 2x or 3x deadlies were so hard it would be "ludicrous" for a DM to use them.... but frankly I throw 2x and 3x encounters at my parties all the time, and even 4x and 5x on occasion
And yes that section can be useful but it doesn't even cover all standard options that are common for players to deal with. People mentioned having ranged characters against melee, is that worth a difficulty drop? Magic Items of course are a big one, while they are "optional" you certainly see them a lot in the various modules....so at least some token lip service to them would be expected (aka players have +1 weapons and maybe armor, what does that do....a least the basics). Or feats, if I allow feats should I just automatically assume 1 difficulty drop, or is it a half one, or does it not change the difficulty?
I respect that a simple system based on CR is not going to be perfect, a simple model will high variance, and a rigorous one would create far more complexity than most are comfortable with. But I can also say having run games for a long time under 3.0,3.5,4e, and now 5e.... that 5e's encounter difficulty estimate is the "worst by far". When I ran deadly encounters in 3.5....my players were sweating. In 5e if I'm not at 2x/3x deadly, its barely a real encounter.
One reason is bounded accuracy prevents monsters from scaling quickly, and so it takes quite a lot of extra oomph to challenge a party. The other is the death save system pads monster offense. Doubling a monster's attack damage on an attack for example will surely blow through your hp quicker but rarely is it enough damage to trigger instant death (past 5th level or so). Therefore when it comes to "finishing off a PC", a monster doing 20 damage is the same as one doing 10. This gives a very large cushion for players and tends to dramatically reduce the potency of greater offense. That is not inherently bad, in fact the "death cushion" is a very nice feature for many players (it also helps reduce the chance that a DM just mows through their party with an oops)....but it does mean the depth of encounters a party can handle is often much higher than the rules suggest.
Aka I wish they had just widened the range, increased them by 1.5x or so, maybe even 2x.