Reproduction steps:
1) Create or open already existing project
2) Switch your code editor to MonoDevelop
3) Change project Scripting Runtime Version to .NET 4.6
4) Create script and open it with MonoDevelop (double click on a script)
5) Try to attach MonoDevelop to Unity
-- Notice that attaching failed with errors in MonoDevelop:

MacOS has 31 errors - each error is about System class. https://gyazo.com/16cb104d342b11b04bd7e251995919fd
Windows has only 1 error:
Error CS1617: Invalid option '6' for /langversion; must be ISO-1, ISO-2, 3, 4, 5 or Default (CS1617) (Assembly-CSharp)

Reproduced with:
2017.1.0b1, 2017.2.0b3

Unity 5.6 doesn't have .NET 4.6

Tested on Windows and MacOS