EDIT: Ehm, forget about that, you havn't asked how to deal with variables!
I never have seen such custom configuration options. At least I can't remember. But for Variables you can write
qmake "DEFINES += MYFEATURE"
qmake "DEFINES += MYFEATURE"
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then you can check it in your pro file with
contains( DEFINES, MYFEATURE ) {}
contains( DEFINES, MYFEATURE ) {}
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and you can use it right in your files
#ifdef MYFEATURE
/*...*/
#endif
#ifdef MYFEATURE
/*...*/
#endif
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