I don't understand because I don't know why some Kexts go in extra and some don't
Most legacy kexts work in /E/E.
Kexts with dependencies can also work in /E/E if you copy its dependencies to the same folder.
Some need mkext in /Extra to work.
I have all "extra" kexts in /E/E
The only changes in /S/L/E are edit in Yukon kext and remove AppleUpstreamUserClient.kext to avoid mouse lag using iTunes.