[Bug]: Application will launch in the app but won't in File Explorer

[MangoDragonHub]

Describe the bug

I'm not 100% sure if this is an desktop environment issue or with the application itself.
I always had issues launching applications with bottles because the applications I run will say it's launching but never launches and doesn't give me any errors or what dependencies its required. However, that's not what I'm here for today.

I'm using this 3D texturing app called Materialize, an Unity-based application, and I launched the app via Bottles since Wine didn't want to open it. I right click on the application in the Dolphin file manager and pressed Open With and selected Bottles. I selected the Windows Application bottle that I made and the application didn't launch. However, when I went to actual Bottles app, went into that Windows Application bottle and ran the executable through there, it works fine.

It's weird that the shortcut way of doing the exact same thing doesn't work, but the long way around does.

To Reproduce

*Might be desktop dependent

1.) Open up to where the application is in Dolphin
2.) Right Click on the app
3.) Choose Choose Open With and select Bottles.
4.) Select the Bottle that you want to use with the application
5.) Cross your fingers and wait if it opens or not.

Package

Flatpak from Flathub

Distribution

Tuxedo OS

Debugging Information

Official Package: true
Version: '51.17'
DE/WM: plasmax11
Display:
    X.org: true
    X.org (port): :0
    Wayland: false
Graphics:
    vendors:
        nvidia: &id002
            vendor: nvidia
            envs:
                __NV_PRIME_RENDER_OFFLOAD: '1'
                __GLX_VENDOR_LIBRARY_NAME: nvidia
                __VK_LAYER_NV_optimus: NVIDIA_only
            icd: /usr/lib/x86_64-linux-gnu/GL/vulkan/icd.d/nvidia_icd.json
            nvngx_path: /usr/lib/x86_64-linux-gnu/GL/nvidia-550-120/extra/nvidia/wine
        intel: &id001
            vendor: intel
            envs:
                DRI_PRIME: '1'
            icd: /usr/lib/x86_64-linux-gnu/GL/vulkan/icd.d/intel_icd.x86_64.json:/usr/lib/x86_64-linux-gnu/GL/vulkan/icd.d/intel_hasvk_icd.x86_64.json:/usr/lib/i386-linux-gnu/GL/vulkan/icd.d/intel_hasvk_icd.i686.json:/usr/lib/i386-linux-gnu/GL/vulkan/icd.d/intel_icd.i686.json
    prime:
        integrated: *id001
        discrete: *id002
Kernel:
    Type: Linux
    Version: 6.11.0-108013-tuxedo
Disk:
    Total: 16757551104
    Free: 16757362688
RAM:
    MemTotal: 31.2GiB
    MemAvailable: 17.8GiB
Bottles_envs: null

Troubleshooting Logs

No response

Additional context

No response

[MangoDragonHub]

I also tried a few games like Rollerdrome and a few Itch.io projects and they won't load unless I go through the bottles app.