Alright, so...

according to your first test and as expected a notification daemon does not seem to be available. According to your report, you do have notification-daemon installed, so running /usr/lib/notification-daemon/notification-daemon in your desktop session should solve that. Desktop environments often include a specific daemon. notification-daemon is Gnome's. Plasma, Xfce, LxQt, MATE, Cinnamon etc. have their own and the respective packages all provide notification-daemon, see https://packages.debian.org/bookworm/notification-daemon. A common choice by folks on i3 and similar is dunst.

As no notification daemon seems to be running, blueman uses its fallback and shows a GTK MessageDialog. Just like any GTK window, they should get decorated by the window manager by default. A simple test in Python (run with python3 -c as before or just in the interactive interpreter), independent of blueman:

from gi.repository import Gtk
Gtk.MessageDialog().show()
Gtk.main()

Boiled down to a GTK Window (MessageDialog is a special case of a Window):

from gi.repository import Gtk
Gtk.Window().show()
Gtk.main()

Both should show decorations, as that's the default (https://docs.gtk.org/gtk3/method.Window.set_decorated.html). I can force missing decoration with:

from gi.repository import Gtk
Gtk.Window(decorated=False).show()
Gtk.main()

Maybe you can make it work with the opposite:

from gi.repository import Gtk
Gtk.Window(decorated=True).show()
Gtk.main()

That's totally unexpected, though, and you seem to have a more generic issue between GTK and your window manager, unrelated to blueman.

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