The gn generator in Chromium in QtWebEngine 5.9.1 does generate invalid ninja files on Windows (due to not escaping ":" in paths). This upstream patch adds support for MSVC to gn to properly escape the paths in ninja rules, so that ninja does not reject the build files.
The second change in the recipe is to set the Python environment properly when running the make step (i.e. craft --make qtwebengine), instead of the compile step (which does not seem to be exist?)
This does not make QtWebEngine to build with craft yet, but after applying this patch I was able to build QtWebEngine in the craft environment by running qmake and jom directly in the source directory. I suppose that with doing some magic (like copying the source files into the build dir and than running non-shadowed build) might make QtWebEngine buildable with craft