Jython's *$py.class files are byte-compiled modules, not extension modules.

There should be a way to disable generation of *.pyo files on command line even if setup.cfg enables it.

IMHO it would make more sense if --optimize-bytecode was dependant on --byte-compile option:
--no-byte-compile                      -> No *.pyc and *.pyo
--byte-compile --optimize-bytecode=0   -> Only *.pyc
--byte-compile --optimize-bytecode=0,1 -> *.pyc and *.pyo (with docstrings)
--byte-compile --optimize-bytecode=0,2 -> *.pyc and *.pyo (without docstrings)
--byte-compile --optimize-bytecode=1   -> Only *.pyo (with docstrings)
--byte-compile --optimize-bytecode=2   -> Only *.pyo (without docstrings)
--byte-compile --optimize-bytecode=1,2 -> Error

Byte-compiled files in Gentoo are generated separately, after installation.