I've just run into trouble with two object files with the same name in MSVC. By default MSVC puts all the object files in the same folder which can result in name classes if you have two CPP files with the same name, but in different folders in the source. This doesn't happen with Xcode, which presumably has some slightly more clever logic.
Would it be a breaking change to have introjucer put:
C/C++ -> Output Files -> "Object File Name" to:
By default into the MS project files? This would make things more consistent cross-platform.