DBusActivatable=true not working for --user install

Using Rocky Linux 9.8.

System-wide install works great. But when installing with `--user`, the application fails to launch when clicking the desktop icon (provided via .desktop file found at `~/.local/share/flatpak/exports/share/applications/org.gnome.Gnote.desktop`)

If I edit the desktop file and change `DBusActivatable=true` to `DBusActivatable=false` under the `[Desktop Entry]`, and log out/in, then the application launches via the icon.

Note: the content of `~/.local/share/flatpak/exports/share/dbus-1/services/org.gnome.Gnote.service`, which I assume it's triggering:

```
[D-BUS Service]
Name=org.gnome.Gnote
Exec=/usr/bin/flatpak run --branch=stable --arch=x86_64 --command=/app/bin/gnote org.gnome.Gnote --shell-search
```

Manually running the Exec command on the terminal gets similar results -- it does nothing for about 30s and then completes, failing to launch the app. Without the `--shell-search` flag it launches fine -- looks like it's for backgrounding the process, so wondering if that's the issue?

Start by comparing the generated ~/.local/share/flatpak/exports/share/applications/org.gnome.Gnote.desktop entry with the DBus service at ~/.local/share/flatpak/exports/share/dbus-1/services/org.gnome.Gnote.service. Reproduce the --user launch on Rocky Linux 9.8 and investigate the --shell-search invocation. Done means clicking the desktop icon launches Gnote successfully without manually editing the desktop file.

Written by the indexing model from the issue text.