This sort of thing doesn't bother me, since I prefer burning Encore build projects from others applications anyway. And now that Adobe has declared Encore as finished as of CS6, I doubt we will see fixes for any old issues.
Literally the problem addressed above is "feature-length projects, the audio goes out of sync several frames towards the end." For most feature length films, there's no audio and black for a second or more from the end. I don't do feature length films and don't burn with Encore for other reasons, so I can't comment. I am not doubting a problem, but it is not clear to me what the problem is.
Sync issues can be introduced for a variety of reasons, some unrelated to Encore, and others that Encore may play a role in.
Also, I don't see how the burn itself can introduce a sync issue. The image build from Encore, the iso, includes the muxed vobs, so how could it? Encore has frequent burning problems, but how could any burn introduce such an issue.