Here's how my build system will do it: the programmer will list default build profiles. Then the build system will generate Visual Studio or XCode files that include all of those default build profiles, but those VS or XCode files will simply call my build system with the correct build profile.
Thus, when a build is run from VS or XCode, my build system is still in full control.
In essence, instead of generating build files for use by other build systems, my build system will generate files to tell VS and XCode how to call my build system. It will tell VS and XCode how to integrate it.