[DanCooper]

Its weird because I dont have any of that artwork addons installed

If an addon or a skin needs additional addons the additional addons will be installed automatically. MQ always needs many addons because it's totally overloaded with functions and features.
 

but maybe I can try installing and see what happens

If no of the addons are installed i whould not install it manually.
 

Just to be sure: if the sync was ok the "choose artwork" menu (as you posted) should index that extra artwork or is skin related?

Yes. It's not skin related. It shows the images that has been found in the Kodi database.
Long time ago the skins searched in the movie folder for additional images and used them directly. But since many Kodi versions all skins should only use images that has been added to the "art" database.
 

Can be that artwork "indexed" or "assigned" to the movie in that menu independently of its showed or not?

This menu is to show and change/assigne artwork to a movie.
 

Any idea about the other issue in audio tracks? I did the ffmpeg "capture" you posted but the output mkv only use first audio and first subs tracks, not all of them.

Nope. I've not tested the ffmpeg command, but it should copy the whole video file and just cut it the the size you set.