As seen at Make a Windows app ready for the Microsoft Store - Code - CMake Discourse windeployqt is deploying the vc_redist.x64.exe which in the case of a Windows Store application doesn't work.

Windows Store requires all binaries to be present in the directory including the C++ Runtime.

This would match the local deployment from Deployment in Visual C++ page. 

The the above link I've documented how one could do it manually (copying vcruntime140.dll and vcruntime140_1.dll from the right place), but windeployqt should allow this usage.