As I noted above, the potential problems aren't really new, given at
least the existence of MSYS. MSYS exists for many years now. Have you
searched the list for problems which have been reduced to the
co-existance of MSYS and Cygwin on the same machine? I didn't, but then
again, I can't remember any of them. If there are some, they are very,
very seldom for sure.
So, here's your next question: Given that there are no or so few
problem reports which could be tracked down to a MSYS/Cygwin
co-existance problem, does that mean the potential problems are
exaggerated, or does that mean we just didn't detect the cause of the
problem? As you can easily guess, I have no answer to this question.