bpo-39769: Fix compileall ddir for subpkgs. (GH-18676)

Fix compileall.compile_dir() ddir= behavior on sub-packages.

Fixes compileall.compile_dir's ddir parameter and compileall command
line flag `-d` to no longer write the wrong pathname to the generated
pyc file for submodules beneath the root of the directory tree being
compiled.  This fixes a regression introduced with Python 3.5.

Also marks the _new_ in 3.9 from PR #16012 parameters to compile_dir as keyword only (as that is the only way they will be used) and fixes an omission of them in one place from the docs.