Using a scope for an instrumentation and mains earth
Yes, the only reason to use 3-prong is safety (but it’s an important reason, don‘t you think?)

And yes, the only reason to use 2-prong instead of 3-prong is to remove ground loops which could affect your measurement. 

But with a differential probe, you can use 3-prong (safety) without ground loop -> that’s the way to go!