Not sure about the third party's audit verdict. But imp, you should verify their suggestion. Perhaps its not required at all. The configuration file should contain the runtime and other configuration related values.
However, if you insist deleting these from your config file, you can do so. But keep in mind that -
On .NET 4.0+ apps, it defaults to v4.0 runtime (then rolls forward to whatever 4.x is installed).
On .NET 2.0/3.5 apps, it defaults to v2.0 CLR.
This usually works fine unless your app was explicitly depending on a particular runtime behavior.