I believe that TIE does the best job at fixing the leveling issues of the game, would it really be hard to make that standalone?
It may or may not be the best at unleveling the game, but everything TIE does add meshes perfectly well with itself. Veritas was very careful with the added NPCs and tweaked creature variants not to get carried away and have stuff that didn't fit. There are no external resources used, so there should be nothing in TIE that looks or feels out of place.
You only get "it doesn't fit" issues when you start mixing content from other overhauls in much the same way throwing TIE into FCOM makes things not fit.
It seems like you're seeking a type of perfection that can't exist. I'm of the firm belief that if you want to play an overhaul, play THAT overhaul. Don't try and wedge them all together because unless you're prepared to put in years of work to sort out the philosophy differences, you'll just have mish-mash.
btw I just ran TES4Edit cleaning on 1.40 in case you need to know:
The Nexus copy is already cleaned - one of the things I did before uploading it there