I ended up fixing this with install_name_tool, but I was wondering if it was possible to add a hook to your script to fix this issue too.
otool -L lib/libPythonQt.dylib
lib/libPythonQt.dylib:
libPythonQt.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
/usr/local/opt/qt5/lib/QtWidgets.framework/Versions/5/QtWidgets (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtGui.framework/Versions/5/QtGui (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtCore.framework/Versions/5/QtCore (compatibility version 5.5.0, current version 5.5.0)
/System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/IOKit.framework/Versions/A/IOKit (compatibility version 1.0.0, current version 275.0.0)
/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/AGL.framework/Versions/A/AGL (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 104.1.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
otool -L lib/libPythonQt_QtAll.dylib
lib/libPythonQt_QtAll.dylib:
libPythonQt_QtAll.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.0)
libPythonQt.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/opt/qt5/lib/QtWebKitWidgets.framework/Versions/5/QtWebKitWidgets (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtWidgets.framework/Versions/5/QtWidgets (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtGui.framework/Versions/5/QtGui (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtCore.framework/Versions/5/QtCore (compatibility version 5.5.0, current version 5.5.0)
/System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/IOKit.framework/Versions/A/IOKit (compatibility version 1.0.0, current version 275.0.0)
/usr/local/opt/qt5/lib/QtWebKit.framework/Versions/5/QtWebKit (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtNetwork.framework/Versions/5/QtNetwork (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtSvg.framework/Versions/5/QtSvg (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtOpenGL.framework/Versions/5/QtOpenGL (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtPrintSupport.framework/Versions/5/QtPrintSupport (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtMultimediaWidgets.framework/Versions/5/QtMultimediaWidgets (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtMultimedia.framework/Versions/5/QtMultimedia (compatibility version 5.5.0, current version 5.5.0)
/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/AGL.framework/Versions/A/AGL (compatibility version 1.0.0, current version 1.0.0)
/usr/local/opt/qt5/lib/QtXmlPatterns.framework/Versions/5/QtXmlPatterns (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtSql.framework/Versions/5/QtSql (compatibility version 5.5.0, current version 5.5.0)
/usr/local/opt/qt5/lib/QtXml.framework/Versions/5/QtXml (compatibility version 5.5.0, current version 5.5.0)
/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 104.1.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)