The AppPool's .NET CLR Version is different from the .NET Framework Version.
The .NET CLR Version 4.0 is the CLR base for the following .NET Framework Versions:
4, 4.5, 4.6, 4.7, 4.8, so having a .NET CLR Version of 4.0 just means you support the above Frameworks, which will run under their deployed framework version.
The .NET CLR Version 2.0 is the CLR base for the following .NET Framework Versions:
.NET Framework 2.0, .NET Framework 3.0, .NET Framework 3.5.
As for the choice of 2.0 or 4.0 depends on the version of .NET does SCCM use, usually SCCM uses .NET Framework version 4.5 or later, so I suggest you use v4.0.
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