Wasn't sure if this was a bug or feature. I leaning towards feature since it's only a bug you're under Lv80:

Blizzard's 'status bar 2' (rep bar when exp bar is active) isn't fading with any frame (tested with global settings) and should be fading out with exp/status bar 1, which is part of the 'StatusTrackingBarManager' frame. Granted, once you hit Lv80, status bar 2 becomes inactive.

Blizzard's 'status bar 2' should be part of StatusTrackingBarManager frame unless it's not possible.

Should be fixed in 1.48.8