Thanks to @heckflosse and @Hombre, LuminanceHDR can be built using MSYS2.
It is still a WIP and they need testers
A new version of W64 installer with align_images_stack.exe and dependencies correctly installed available here
https://drive.google.com/open?id=19L6jI85Q_MAXZhQkUBNuEuUrqUqFPxjA
It can be installed where you want and should not interfere with official stable version.
Please report test results at Issue 78