I am aware of that, but I wanted to point out that the DMG explicitly tells you that using PC race and class is one of the three ways to make NPCs suitable for an encounter, the other ways being the "quick way" (minimal stats, basically fixed AC/HP/attack/damage/DC) and the "monster way" (full stat block, built from the ground up). It doesn't tell you that the "PC levels" way doesn't work.
It works fine, it's just less smooth to start with a CR in that case.
And of course the problem is not in building the NPC. In fact it's about as easy (or even easier) than creating is the "monster way". The problem is that the DMG tools work more for figuring out the CR after the design, while the CR is supposed to be your starting point.
It's fair to say that it's hard to start with a CR and get an on-target PC-style NPC, but I think that criticizing 5e for that fails to appreciate that this was likely one of the prices the designers paid for having PC rules that are more flexible.
It might be useful to contrast 4e's ADEU powers system with its strict, granular balance - every power of a given level and usage doing fairly comparable initial damage (before role considerations are brought in), and players locked into taking a certain number of "attack" powers vs. other powers. This system could allow for easy level-to-CR determination - a character of a given level has a certain damage output, HP, AC, attack rolls, etc. that is within fairly consistent norms, so you can say Level 14 is roughly CR 10 or whatever.
But the moment you have the ability to swap
mage armor and
magic missile for
comprehend languages and
charm person (or even greatswords and shields for twin daggers) you're looking at a game where character combat capability is not on a tight curve. You can only say that a character of a given level with particular abilities is a given CR. Which means that you need to build the NPC anyway - you need to choose its abilities before you can determine what CR it is. Simple level isn't going to tell you much.
So you have a trade-off: how flexible do you want character creation to be vs. how easy you want it to be for level to be a precise measure of hp/ac/attacks/save DCs/dpr.
With those competing interests, I think flexible character creation is the appropriate winner, given that it is the more exposed mechanic (meaning, everyone who's not just a DM is going to interact with character creation at an early point in their game experience, but only DMs going beyond the MM will need to worry about the CR of classed NPC's). This is especially true with a broad CR range - where if you have to whip up an enemy mage and she's too weak, you can maybe just throw two or three or add some orcs or whatever and it'll be fine.
I'd still appreciate an "MM of NPC's," personally, but I don't fault 5e for not being able to say "A level X character is CR Y" in a simple and obvious way. In order to achieve that, more important goals like character flexibility would need to be sacrificed.