We’re running into an Intune issue where a Win32 app with a dependency sits at "Download Pending"

I can at least answer your main question. This isn't explicitly stated in Microsoft's documentation: https://learn.microsoft.com/en-us/intune/intune-service/apps/apps-win32-add#step-5-dependencies but in testing, Yes you can install an app with install behaviour set to User and it will automatically deploy a dependant app with install behaviour set to System. 
 
I have a very similar situation that has made me question everything. Both apps install and are detected successfully when run in sequence separately.  When the USER win32app is installed with a win32app dependency not already met, the deployment appears to hang indefinitely in "Download Pending..." when navigating back to company portal the status resets to "Install". Automatic Install doesn't trigger when enabled. When automatically install is disabled the status doesn't show that the assigned dependent System app is missing. For me this effects a specific app deployment and multiple test devices. The deployment failure is never logged in Intune. 

In my case, the deployment works with other win32apps system apps set as dependencies, so I believe the issue lies with the dependant System app but have yet to pin point the difference in the app deployments in Intune Management Logs.