As noticed in x11-toolkits/qt5-charts we never corrected the way in which qmake sets the pkgconfig path for Qt5-modules. Instead there was a sed-call on the generated Makefiles in bsd.qt.mk in the target qt-pre-install.
This diff modifies devel/qmake5 to set QMAKE_PKGCONFIG_DESTDIR to ../libdata/pkgconfig from the default pkgconfig.
As we split Qt-base into multiple ports, simply patching devel/qmake5 is not enough, as the other base-ports will use the file from inside the tarball. Therefore add it as an extrapatch for the Qt-base ports.
As this affects the same file extrapatch-libtool in devel/qt5 touched, rename this one and add a hunk to do this change too.