[Bug]: Launch options not honored when application is launched from Desktop Entry

[eomanis]

Describe the bug

I have an application that requires the "Virtual Desktop" launch option to be usable:

However, when I start the application from its dedicated Desktop Entry that was created using the "Add Desktop Entry" feature, the "Virtual Desktop" launch option is not active.

The "Exec=" line in the .desktop file looks like this:
Exec=flatpak run --command=bottles-cli com.usebottles.bottles run -p TheProgramName -b 'Bottle Name' -- %u

I have attempted to find a bottles-cli command line argument to enable "Virtual Desktop", but I could not find one.
The output of flatpak run --command=bottles-cli --help did not show such an option.

There is already a very similar but closed bug, maybe this is a regression.

To Reproduce

1. Install some graphical Windows application in a new bottle
2. Set the launch option "Virtual Desktop" for its "Programs" entry in the Bottles user interface
3. Launch it from within the Bottles user interface and see that the "Virtual Desktop" feature is active
4. Create a dedicated Desktop Entry using the "Add Desktop Entry" feature
5. Launch the application from the dedicated Desktop Entry and notice that the "Virtual Desktop" feature is inactive

Package

Flatpak from Flathub

Distribution

Arch Linux

Debugging Information

Official Package: true
Version: '51.15'
DE/WM: gnome
Display:
    X.org: true
    X.org (port): :0
    Wayland: true
Graphics:
    vendors:
        amd:
            vendor: amd
            envs:
                DRI_PRIME: '1'
            icd: /usr/lib/x86_64-linux-gnu/GL/vulkan/icd.d/radeon_icd.x86_64.json:/usr/lib/i386-linux-gnu/GL/vulkan/icd.d/radeon_icd.i686.json
    prime:
        integrated: null
        discrete: null
Kernel:
    Type: Linux
    Version: 6.12.1-arch1-1
Disk:
    Total: 16788164608
    Free: 16787992576
RAM:
    MemTotal: 31.3GiB
    MemAvailable: 26.8GiB
Bottles_envs: null

Troubleshooting Logs

No response

Additional context

No response