Setting up and managing device configurations using Intune
I was able to work out the issue with some help and resolve it by adding some registry keys to allow the configuration app to function using Internet Explorer even though it should be using the Webview2 modules.
In location:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet Explorer\Main\FeatureControl\FEATURE_BROWSER_EMULATION
Add DWORD (32-bit) value:
PFXCertificateConnector.exe with decimal value 11000
Update prevhost.exe decimal value to 11000
In location:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet Explorer\Main\FeatureControl\FEATURE_DOCUMENT_COMPATIBLE_MODE
Add DWORD (32-bit)
PFXCertificateConnector.exe with decimal value 10000 (11000 should work as well but we didn't test this)
Hope this can help someone else experiencing the same issue.