I was looking into this and found a way that works (in qt 4.7.2) by customizing qt with a qt.conf file.
In my case, I added a qt4-4.7.2/bin/qt.conf (I think it must be in the same place as the qmake executable)
With the following contents:
[Paths]
Prefix = c:/my_path/to/qt4-4.7.2
and the qmake -query started returning the proper paths!
See: http://qt-project.org/doc/qt-5.0/qtdoc/qt-conf.html for more details
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