Managed to fix it myself, but with Gnome Extensions. I suspected the issue started when I installed Gnome Tweaks. But maybe it was Gnome Extensions.
I opened Gnome Extensions, scrolled down to User Themes, turned it on and in the selection menu selected Pop Dark. It defaulted to default. Once I did that, the Applications window looked right again. Why it only affected the Applications window, I have no idea yet. But now it looks right.
I’m trying really hard not to go down the rabbit hole of themes, because I know Cosmic is coming. Just haven’t seen any ETA on that other than maybe an alpha later this month.