There is a really well written article about Nuitka written by Tom Sheffler.
It inspired me to finally become clean with __file__ attributes in standalone mode. Currently it points to where your source was when things were compiled. In the future (in standalone mode, for accelerated mode that continues to be good), it will point into the .dist folder, so that the SWIG workaround may become no longer necessary.
Thanks Tom for sharing your information, and good article.