This post explains the major difference of using Win32 and LOB app in Intune purely based on my experience when I was trying to find the way to push the apps for both AAD registered and AAD joined devices.
Apart from all the other features of win32, win32 app didn't push for the devices which are just joined type as AAD/WPJ Registered. Win32 only worked for the devices which are just joined type as AAD Joined.
But at that time LOB app worked for both the devices of AAD/WPJ registered and AAD joined. But you should wrap up the app into .MSI to support for LOB app pushing. its an additional configuration and you have to configure the command lines of app pushing when wrapping it up whereas win32 can be configured in the intune when pushing the app.
What has changed?
There was an update from MS. As of October 2020, win32 app can be pushed to both AAD/WPJ registered and AAD Joined devices as well.
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