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As a post-processing step, rpmbuild will attempt to byte-compile any .py files it encounters, and the results must be listed in the %files manifest. [1]
This is done by the script brp-python-bytecompile, which uses the compileall module. However, my guess is that it's not using the correct version of python when invoking "compileall", which would explain why it's using the pre-PEP3147 location for the .pyc/.pyo files.
Can you run "file" on the .pyc files and confirm which version of Python they're bytecode for? My guess is that it's bytecompiled them with /usr/bin/python, rather than your local build of python.
Some notes: In older versions of RPM, brp-python-bytecompile took a single optional argument: the python interpreter to use, defaulting to /usr/bin/python. I generalized this to support multiple defaults when adding Python 3 support to Fedora: see https://bugzilla.redhat.com/show_bug.cgi?id=531117 That patch could be generalized to support /usr/local/lib.
[1] In Fedora we do this using "__os_install_post", which is defined
in /usr/lib/rpm/redhat/macros (from the redhat-rpm-config package),
which has the invocation of /usr/lib/rpm/brp-python-bytecompile So it could be possible to override the python interpreter to use by redefining __os_install_post