CR really is a guess based on an "average" party, but the game has been trying to pass it off as absolute law for at least a couple editions. If the DMG could do better about relaying that it's a ballpark value to start with I think it'd help a lot of tables and new DMs. Problem is, with this revision they seem to be doubling down on it being an absolute principle, which I think is a bad idea.
There's never going to be a perfect CR system, there can't be. Every group is different and the current CR guidelines aim towards the bottom of the barrel. I use a slightly different calculation for encounter building but when I do, while also double checking monster capabilities such as flying, my results are pretty accurate.
It's not like I'm doing anything magic or that I'm some genius level monster combat tactician, it's just finding the right balance for the group.