I noticed in all the changes with FLAC in the tagger I use, same changes were made with Vorbis in same sentence (there was a few other mentions other than I quoted). I don't know if my tagger does use extra id3 tagging, but do recall they removed one option for tagging FLAC to comply with FLAC changes.
Windows only guide lol Unfortunately my tagger does not specify or give options about whether it is using vorbis comments or id3 tag.
I'd like to know more about that. There was Ogg Vorbis works done for mac osx for each of iTunes & QuickTime. However work has not been continued on those projects in a few years at least. I used the vorbis plug-in option for iTunes on my previous mac.
Many programs have limitations of some sort or another. Looks like Foobar2000 has some limitations of its own. Lack of foresight in their programming.

As I hinted at earlier, there are apparently different versions of FLAC. Perhaps the earlier version encoders cannot cope with the added information (earlier version flac libraries). I use Switch for my encoding. I can say Toast Titanium, the best burner program for Mac appears to have no problem with my FLAC files (just tried burning some.)

But points taken.