Major Description
The behaviour of the old importer is such that if the PythonPath directive has been used in the same or parent configuration context, then any physical directory corresponding to where the Python*Handler directive was used, is not added to sys.path.
The new importer currently preserves the above behaviour, but since the new importer does not actually add the directory associated with the Python*Handler directive into sys.path, it doesn't seem to make any sense that setting PythonPath should cause the directory the Python*Handler directive is associated with to be ignored.
Thus propose that PythonPath should be kept quite distinct from directories in document tree for which Python*Handler is specified for and setting PythonPath will would no longer cause directory Python*Handler directive is specified for to be ignored.
Overall, this should actually eliminate unexpected behaviour whereby user sets PythonPath and then finds their modules in document tree can't be found. The only solution to this with the old importer is to add the directories in the document tree explicitly to PythonPath directive.
If there is some valid reason that the new importer should never look in the document tree for modules, then it would be better handled by some sort of PythonOption rather than it be a side effect of having used the PythonPath directive.