Get the UUID of the default profile
Substitute that value in to the second command to enable transparency level
$ dconf read /org/gnome/Ptyxis/default-profile-uuid
'3aae5a177777aa966b1fd63467153e2d'
$ dconf write /org/gnome/Ptyxis/Profiles/3aae5a177777aa966b1fd63467153e2d/opacity 0.85
I ended up installing the flatpak version and used this guide to set the transparency on the flatpak: https://mmilburn.dev/blog/transparency-in-ptyxis/
I have no idea why the rpm version on my Silverblue install stopped actually being transparent despite being set.