I have a Kit configured for cross-compilation:

Device type: Generic Linux Device
Sysroot: /home/julien/vqm_build/build/rootfs
Compiler: /home/julien/Tools/gcc-...-gnueabihf/bin/arm-linux-gnueabihf-gcc
Qt version: Qt 5.6.2
CMake tool: System CMake at /usr/local/bin/cmake
CMake generator: <none> - Unix Makefiles, Platform: <none>, Toolset: <none>

This configuration works properly when using a qmake .pro file. However this configuration fails to work with a CMakeLists.txt file and results in linking errors ("libraries cannot be found"). I found that it fails to pass the sysroot variable to CMake. This is confirmed by checking the CMake configuration field in the Kit:

CMAKE_CXX_COMPILER:STRING=%{Compiler:Executable:Cxx}
CMAKE_C_COMPILER:STRING=%{Compiler:Executable:C}
CMAKE_PREFIX_PATH:STRING=%{Qt:QT_INSTALL_PREFIX}
QT_QMAKE_EXECUTABLE:STRING=%{Qt:qmakeExecutable}

Adding the following line resolves the linking issues:

CMAKE_SYSROOT:STRING=%{SysRoot:FilePath}

Apparently this is a know issue:

https://bugreports.qt.io/browse/QTCREATORBUG-16155

The patch is available but was never pushed and it is unclear why. I understand that the OP had other issues which were not solved by this fix. However I think the fix is legit as the sysroot is a critical variable when doing cross-compilation that needs to be passed to CMake.