Sorry, it looks like I was confused about how CD Extra discs work with CDDB. For some reason I thought the disc ID calculation ignored the extra session data track for CD Extra discs, but it turns out that behavior's not standardized;
some databases intentionally ignore it and some programs don't include it because of the way they read the disc, but other programs do include the data track with the audio tracks. I looked up some CD Extra discs on freedbtest and found more than one example of it having two different tracklists for the same CD: one submitted with the data track and one without.
It looks like most CD Extra submissions we have here don't include the data track, but I'd have to check with Secret Squirrel to verify we're doing about those.