It would be nice to be able to set the INSTALL_ROOT that gets passed to the qmake generated Makefile(s) from the .pro file.
That would save the bother to have to pass it as a command line argument at build time.
The problem is that when Qt is crosscompiled and installed with INSTALL_ROOT, then when the application is compiled it is looking for a wrong place for headers. Maybe not pro file is the right place, but something similar like it is in Qt5.1 with the sysroot option.

http://www.qtcentre.org/threads/30449-How-to-build-and-install-Qt-apps-on-cross-compiled-embedded-targets

Of course there is a workaround to have 2 installation, but that's not so elegant.