The polkit's in Portage only support .rules files now. The ones using .pkla files are gone. So please clean up the networkmanager and modemmanager files to only install .rules file, and punt the .pkla cruft. Do this both, in gentoo-x86 and overlay. Thank you.
You can adjust polkit dependency to latest stable >=0.107 to enforce upgrade.
Looks like latest versions of this packages no longer install them