I'm kind of surprised Adobe tried to modify the font at all. It's a copyrighted font that belongs to Linotype.
So, if I understand correctly, even if I install an OpenType PostScript copy of the font, the system font will override that and I won't be any better off?
If an OT PS version has the same internal names, then yes, you won't get anywhere.
In my little test, I changed the internal names of one font and saved that to an OpenType PostScript font so I could activate it alongside the already installed system font. Saw that it worked, and then deleted it.
Per the above about hinting between the font types, TrueType has lots of hinting since it all has to be part of the font. PostScript has minimal hinting within a font and the PS interpreter does the majority of the hinting work. So, when I saved a TT version of the font out to OT PS, FontLab basically stripped all of the current hinting and replaced it with automatically applied PS hinting. Which eliminated the u issue in the process.
What happened overall is the apps that didn't display an issue with the alignment, those apps were paying attention almost entirely to the font metrics, and little to the hinting. Adobe's apps do kind of the opposite by giving equal weight to both the metrics and hinting to determine how the letterform should be presented.
Making sense of internal names is much easier if you see it. Here's the naming for Avenir Next Condensed Regular:
Note the family name. Every font in this set (regular, bold, italic, etc.) has the same family name, which causes them to appear as a group in your font lists:
I included some of the Bodoni fonts in the screen shot so you can see the two bottom ones must have different family names, which is why the fall separately in the list instead of being grouped inside of Bodoni 72, or Bodoni 72 Oldstyle. I didn't actually look, but I don't need to in order to understand why neither is in a previous group.
The family name wouldn't be the issue. That's just for grouping fonts in a list. If a PostScript version had any internal names identical to the Full name, PostScript or Style group names seen above, then you'll have a conflict with the system installed TrueType version and it won't work.
The good news (sort of), is there are OpenType PostScript versions of Avenir that do work since they have different internal names.
The problem will be finding a legal copy. Adobe's Font Folio 11 used to include AvenirLTStd in 12 styles. None of them condensed.
If you find a legal way to purchase the previous 22 font set of what used to be AvenirNextLTPro fonts, those would work. Otherwise, a trip to Linotype would be necessary.
They sell their fonts through Monotype and MyFonts. And not cheap. It's now 40 faces, and the Condensed Regular font alone is $98. And I can only assume these won't have the misalignment issue. But at least they seem to be the same as the older set of 22 OT PS fonts I have.
A lot of money, I know, but I don't see a cheap or easy way to avoid the Apple included TrueType fonts.