The lots of libraries problem is more or less solved by the KDE Windows project. The emerge system can build pretty much all the dependencies for a big project like Krita out of the box, both with mingw and msvc. There are even two options: one can download most of the dependencies as pre-built binaries, the other will build everything for you.
You'll end up with a tree that looks a bit like a standard unix tree: rootdir/bin, rootdir/lib and so on. From there to packaging the software for an installer is a matter of simply copying the right files to your installer.
If you use kde libraries, then the system is smart enough to make it possible to co-install two kde-based applications and run them at the same time. But even if I would work on a pure-Qt application that needed libraries like lcms, I would still use this system to get all those dependencies ready and in place.