As mentioned in the comments.
$PATH in Linux is used to find a executable. In this case that's Python.
After this executable is found, it will be executed "in" the current working directory and work from there.
Meaning when Python gets the parameter one/toto.py it will start looking from ./ after your folder and file.
You could create a wrapper script, place that under /usr/bin/mywrap.py, mark it as a executable and utilize for path in sys.path: and try to find your module and dynamically import it and do a "hand over" to it.
There is no magic in the Python binary that will travers $PATH since this is a shell variable used to find binaries in the operating system. Much like PATH in windows is used for the same purpose.