The macro can differentiate between left/right by using "mod:lctrl" or "mod:rctrl" for example instead of "mod:ctrl" which does not care if it's left or right. That is, WoW does make the distinction between left and right modifiers, but the macro he pasted is ignoring the left/right distinction:

/target [mod:ctrl,mod:shift,nomod:alt,target=Twymana][mod:ctrl,mod:alt,nomod:shift,target=Twymanb][mod:alt,mod:shift,nomod:ctrl,target=Twymanc][mod:ctrl,mod:alt,mod:shift,target=Twymand][mod:ctrl,nomod:alt,nomod:shift,target=Twymane]
Keyclone had, or has, an issue with the right-modifiers though. (I have no idea if it was fixed or not)