Pop-up/context menus appear underneath windows on the scratch layer

[Cwiiis]

Describe the bug
Right-click menus in apps such as gnome-terminal or Firefox will appear underneath windows on the scratch layer.

To Reproduce
Steps to reproduce the behavior:

1. Open any app (for example, gnome-clocks) and put it on the scratch layer
2. Open another app with an easy-to-access context menu (for example, gnome-terminal)
3. Place the first window over the second window
4. Activate a context menu in the first window to the left of the second window

Expected behavior
A context menu appears, either not obscured by the window on the scratch layer, or over the top of the window on the scratch layer.

Screenshots

System information:
Distribution: Fedora Linux 43 (Workstation Edition)
GNOME Shell: 49.2
Display server: Wayland
PaperWM version: 49.0.0
Enabled extensions:

• paperwm@paperwm.github.com
• start-overlay-in-application-view@Hex_cz
• hidetopbar@mathieu.bidon.ca
• appindicatorsupport@rgcjonas.gmail.com