Intermission Portabox/Bomb support is in for the next update, as well as changing the scenes between Area 5 and 6 to "intermissions" instead of "cutscenes," since I guess they are.
Hmm, I guess you're right about the Levvies. The way I coded it, it made sense to have Unmute gates auto-activate them (getting them Muted is like forcing a toggle-off and disabling the ability to toggle them back on), but I should be able to rework it.
Mute gates don't actually disappear, the pattern of the pause cover just overlaps them completely because they're made entirely of X's.