When running with -Wall then it will warn about some variables being replaced in the prf files. The following output is what gets shown:

WARNING: Operator=(MANIFEST_DIR) clears variables previously set: c:\work\git-depot\qt\oslo-staging-1-47\mkspecs\features\win32\embed_manifest_dll.prf:1

WARNING: Operator=(QMAKE_RCC) clears variables previously set: c:\work\git-depot\qt\oslo-staging-1-47\mkspecs\features\qt_functions.prf:90
WARNING: Operator=(QMAKE_UIC3) clears variables previously set: c:\work\git-depot\qt\oslo-staging-1-47\mkspecs\features\qt_functions.prf:90
WARNING: Operator=(QMAKE_RCC) clears variables previously set: c:\work\git-depot\qt\oslo-staging-1-47\mkspecs\features\qt_functions.prf:90
WARNING: Operator=(QMAKE_UIC3) clears variables previously set: c:\work\git-depot\qt\oslo-staging-1-47\mkspecs\features\qt_functions.prf:90
WARNING: Operator=(QMAKE_RCC) clears variables previously set: c:\work\git-depot\qt\oslo-staging-1-47\mkspecs\features\qt_functions.prf:90
WARNING: Operator=(QMAKE_UIC3) clears variables previously set: c:\work\git-depot\qt\oslo-staging-1-47\mkspecs\features\qt_functions.prf:90

The first warning at least can be rectified by doing CONFIG -= embed_manifest_dll in the embed_manifest_dll.prf file (and doing the reverse in the exe.prf)