Hi,
This is caused by a regression in v3.6 where the engine is not detecting the correct version of .NET installed on the system.
Detecting the newer versions of .NET is often difficult because these frameworks are usually released from Microsoft without any guidance on how to accurately detect them. The guidance usually comes later down the line (thankfully, it's now here).
NCrunch doesn't require you to use v4.6.2 for your projects. The error you're describing is for the engine process. NCrunch needs to use a specific version of .NET to host the engine process, which should ideally be aligned with the .NET version used by Visual Studio. When it initialises the engine, NCrunch tries to identify whether v4.6.2 is installed. If it is, the engine will be loaded under v4.6.2 instead of v4.6.1.
There is no need for you to change the version of .NET you are compiling against. You should never need to do this for NCrunch. The problem you're facing is that the tool has a flawed dependency on v4.6.2. As long as you have v4.6.2 installed, all should be well. This will be fixed in v3.7.