Oh Snap!

[claydoh]

At least in "traditional" Firefox's settings one can choose what should happen with a PDF:

But does not explain or fix the popup (from xdg-portals, NOT firefox) missing window decorations, and can't be closed normally.

This would be happening in a deb version of firefox as well, I'd wager, since both call the same xdg-portal system for this file association selection.
Of course fixing the PDF file association will help here - for that specific filetype.

[Schwarzer Kater]

I wrote "at least in traditional Firefox", because I had no Snap version at hand and was not sure if it had the same options in its settings.
And sorry, perhaps I did not read/understand well enough what the problem was…

[claydoh]

I did not read/understand well enough what the problem was…

Same here, I woke up a little later lol