When configuring static build of Qt and not using prefix, the default paths are Linux paths. After configure, the following message can be seen:
Qt will be installed into '\usr\local\Qt-5.9.1'.

The used configure command can be simple as:
configure -static -commercial -confirm-license -nomake tests -nomake examples

When using the qmake from this build, qt modules cannot be found, qmake debug gives this kind of log:
DEBUG 1: C:/Qt/5.9.1/Src/qtbase/mkspecs/features/qt_config.prf:26: QT_MODULE_INCLUDE_BASE := /usr/local/Qt-5.9.1/include
DEBUG 1: C:/Qt/5.9.1/Src/qtbase/mkspecs/features/qt_config.prf:27: QT_MODULE_LIB_BASE := /usr/local/Qt-5.9.1/lib
DEBUG 1: C:/Qt/5.9.1/Src/qtbase/mkspecs/features/qt_config.prf:28: QT_MODULE_HOST_LIB_BASE := /usr/local/Qt-5.9.1/lib
DEBUG 1: C:/Qt/5.9.1/Src/qtbase/mkspecs/features/qt_config.prf:29: QT_MODULE_BIN_BASE := /usr/local/Qt-5.9.1/bin

Using prefix in configure fixes this issue.