Hi, thanks for posting and for taking the time to try out NCrunch!

As NCrunch monitors all test coverage throughout a solution, your test projects are included in this coverage. Tests do, physically, cover themselves. In many cases the coverage markers on the test can be useful as they allow you to easily analyse complicated test code to see where it is being executed. They also allow you to analyse performance issues inside the test. For this reason, the vast majority of people prefer to have the markers showing next to their test code.

If you find this confusing or it doesn't fit with your view on how the product should work, you are correct in your understanding that turning off the 'Instrument output assembly' option will remove the coverage markers from your test project.

Yes - the instrumentation is required for impact analysis, so you'll find that switching it off will take away some of the intelligence of the engine in its test prioritisation.

There are a couple of settings you may find useful in changing the manner of build/test execution. Have a look at sliding build delay and custom engine modes.