@MissouriSpartan Thanks for posting in our Q&A.
For this issue, I have an idea for reference. We can write PowerShell Scripts that contain installing the application and copying certain items into certain directories. Then we can package the PowerShell Script and the MSiX package as (.intunewin) file format and deploy it to the device via Win23 app.
For deploy win32 app, we can read the following articles as a reference.
https://learn.microsoft.com/en-us/mem/intune/apps/apps-win32-prepare
https://learn.microsoft.com/en-us/mem/intune/apps/apps-win32-add
Thanks for understanding.
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