Then, the developer needs to write his own makefiles and hammer autoconf and stuff into working right. This is the hard part, and it's where I gave up when trying to port Miranda Instant Messenger with Winelib even though it worked in MinGW. There are many other open source Windows apps out there that I'd like to try porting (say, eMule), but they're currently all written in Visual Studio and getting Visual Studio support into Winelib has been on our perpetual todo list for some years now.
I doubt SCons will help here in any substantial way. Its chief appeal seems to be to people who like using python for everything, and who like badmouthing make. - Dan