[Wintermute0110]

Thanks for shading more light. By now, the easiest answers were hardest to get.
So far I managed to build the emulator cores using your option 2) but since I have my kodi installed from ppa, under the prefix /usr, and owned by root, I wonder where should I copy the bin-kodi contents. I copied bin-kodi/lib/kodi to /usr/lib/x86_64-linux-gnu/kodi and bin-kodi/share/kodi to /usr/share but I'm running Kodi as kodi user, and now I have problems with getting my gamepad working in games. When I launch eg Super Mario Bros, kodi.log says
ERROR: GetDirectory - Error getting /usr/share/kodi/addons/peripheral.joystick/resources/buttonmaps/xml
ERROR: AddOnLog: Joystick Support: Error opening /usr/share/kodi/addons/peripheral.joystick/resources/buttonmaps/xml/application/Keyboard.xml: Failed to open file
Maybe I should have copied the addons somewhere to /home/kodi/.kodi ?

It's not just copying the binary .so file, the binary addon has some other supporting XML, PNG, etc. files. You can have a look at a packaged Windows binary addon, for example this, to get an idea of what you need to copy. I think it is not a good idea to copy files you have compiled into /usr/, you can harm your system if you do something wrong.

The other alternative, by far the easiest, is that you compile both Kodi and the binary addons, and execute Kodi as in the tutorial instructions. Note that you can have both the Kodi PPA and your compiled Kodi installed in the same machine. Keep in mind that both Kodis will use the same /home/kodi/.kodi user data directory, but this should not be a problem at all.