@Anarcat You'd need a pinentry that uses e.g. layer-shell protocol to become kind of a system modal dialog guaranteed to be on top of all apps. It could even be triggered by gnome3 pinentry which just uses gcr underneath.
phosh (Wayland) does it like that (but won't work with sway (for reasons unrelated to this issue)):
@Anarcat …that seems to do basically what I described but will have a bit of a hard time landing in Debian.
@agx yep, hence that "why can't i have nice things" post on mastodon :p