HOT DIGGITY I THINK I HAVE IT. And trust me to find it half an hour after posting, after several days of trial and error and yelling at the computer haha.
It was the most obscure setting, and no idea how this was even checked to begin with/why this previously didn’t affect scenes in 5.4 versions…
The solution looks like it was to disable Alpha Output in the Default Settings of your Project Settings and that seems to have eliminated the issue*. Woohoo!