I have a Mac Mini I recently got; To make it easier to deal with, I reversed the control and command keys in settings on the mac. When I use a keyboard local to the mac, control-Key works just fine as command-key used to. and vice versa (for example ending a console program with command-c now instead of control-c; or saving a document with ctrl-S instead of command-S)
However, when I connect to the mac through teamviewer (from windows), the keys are still mapped so control is control and command (windows-key) is command. It doesn't respect the reversed settings in the keyboard.
(png image of mac keyboard settings)