This is similar to QTBUG-59565.  It had the same messge: ERROR: You are not licensed to use this software.That issue was specific to the beta version and the resolution for it does not apply here.

For version 5.9.1 commercial license, The following is the output I get when using ./configure as follow:

 
pmcude@localhost Src]$ sudo ./configure -static -release -no-compile-examples -nomake tests -prefix "/home/pmcude/Qt570static" -qt-zlib -qt-pcre -qt-libpng -qt-libjpeg -qt-xcb -qt-xkbcommon -qt-freetype -make libs -opengl desktop -commercial
+ cd qtbase
+ /home/pmcude/Qt5.9.1/5.9.1/Src/qtbase/configure -top-level -static -release -no-compile-examples -nomake tests -prefix /home/pmcude/Qt570static -qt-zlib -qt-pcre -qt-libpng -qt-libjpeg -qt-xcb -qt-xkbcommon -qt-freetype -make libs -opengl desktop -commercial
Creating qmake...
.Done.
Error: Qt license file was not found!
Note: Also available for Linux: linux-clang linux-icc
ERROR: You are not licensed to use this software.