If you switch to "GUI application", the IDE will use whatever compiler option is correct for the compiler you have chosen, and this will be updated for future releases, too. So this is the correct way to do it. It will work with every compiler that is supported. Always. (Well, unless there's a bug.)
About the "-mwindows is deprecated" story, let's suppose I post "I think the -O2 and -O3 switches are deprecated" on this forum. Will people stop using it them because of this? :lol:
I mean seriously, there is no statement regarding that deprecation on either the gcc, the MinGW, or the cygwin site (at least neither Google nor a hand search found it). I would say that if anyone is an authority on that matter, it is those three, and certainly they would make such information public? The only quote I could find that really said -mwindows was deprecated was some random person on an Allegro forum, and he was not even certain about it!