codesign now signs reqursively app bundles but it fails Qt Frameworks.
codesign -f -s "3rd Party Mac Developer Application: .." --entitlements sample.entitlements sample.app
sample.app: bundle format unrecognized, invalid, or unsuitable
In subcomponent: sample.app/Contents/Frameworks/QtCore.framework

Current framework layout
QtCore.framework/
QtCore.framework/Resources
QtCore.framework/Versions
QtCore.framework/Versions/5
QtCore.framework/Versions/5/QtGui

If move Resources folder into Versions/5 and copy also Info.plist from Qt sources and create links to latest version, codesigning succeeds

Target layout
QtCore.framework/QtCore -> Versions/5/QtCore
QtCore.framework/Resources -> Versions/5/Resources
QtCore.framework/Versions
QtCore.framework/Versions/5
QtCore.framework/Versions/5/QtCore
QtCore.framework/Versions/5/Resources
QtCore.framework/Versions/5/Resources/Info.plis