WinTuner is an app that packages, and deployes thrid party apps to Intune. It's completely open-source so you could verify what is does and you can even improve it yourself.
Command line interface
Currently WinTuner is only available as a cli so go ahead and check that out.
We are working hard to also provide you with a library, so you can easily start packaging apps right from your own C# application. This is not yet available to download, so you'll have to wait a little bit longer.
WinTuner is currently a CLI built in dotnet, but since it's really a tool that is used by system administrators, a PowerShell module feels like a better fit. That is why there is a WinTuner PowerShell module on the roadmap. No promises though!
Since everything is already written in C#, and you can create so called binary PowerShell modules (which are PowerShell modules that define the Commandlets in C#). It's just another way to call the same C# code.