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
@FlexibleToast I just ran all of the available updates on Fedora 41 on my laptop, restarted, and transparency is still working here, so I am not sure how to help.