As someone who remaps their keyboard before the OS gets to it, I can confirm it is awesome to access remote-desktops/virtual machines with my beloved Colemak mapping and just leaving the other side mapped to qwerty.
I would like to add that windows and OS X play nice with each other regarding keyboard mappings, it is really only a minority of keys that might cause some issues.
One example of a difference is Home/End, those keys behave a little differently on OS X than on Windows. Sometimes you won't be able to go to the beginning of the line with Home and you'll need to type cmd+left (a little vexing and squarely Apple's fault).
Another is the "Home/Menu" key for mobile devices, no idea what that is mapped to on desktop keyboards
But in general, this switching between OSes with only one key map should not pose insurmountable problems.