There is likely no difference of qmake itself, but using a different qmake means linking against a different Qt.

I.e. when qmake generates the Makefiles, it will use the include and library paths of "its" Qt.

The Qt you have in /usr/local/TrollTech/QT4.8.6/ might have been built differently, e.g. without touch support.

Cheers,
_