After hitting some weird PyInstaller bugs, I gave up and started compiling Python myself. One interpreter for every project. Shell scripts to set the paths.

After hitting some weird PyInstaller bugs, I gave up and started compiling Python myself. One interpreter for every project. Shell scripts to set the paths. All libraries go directly in site-packages, not some other layer. A little more complicated at the outset, but this approach has yet to let me down. And compared to the nightmares I was trying to fix, building Python is dead easy.