When I specify an application DESTDIR in the project file
by means of $$[VARIABLE], qtcreator fails in producing
a correct (one that points to destdir) run configuration
(see snapshot). It's likely the same will happen when
I use a system env-variable.

The reason for this mechanism is to be able to use qmake
environment variables (qmake -set) to have something which
is globally available across my project. I know that for
the example I provided it's quite useless...