Hello ilya,
Firstly congrats on the machine, those panels sure do look "it and a bit"
It seems to me that the reason you are getting a lot of marks on the floors of the pockets are due to the panel vibrating. You can really hear it in the videos quite well. Ultimately vibration hurts everything.
I see it is screwed down at the ends leaving the middle not hard against the table/scrap piece.
No amount of final cuts will really help in situations like this.
Are you able to provide more opportunities for clamping? Either more screw holes or you may have to resort to placing many clamps over the panel and writing Z axis lifts to clear them.
An MDF panel of the same size but with the holes a bit bigger would be a good way to prevent clamp marks/scratches from getting onto the alum panel
Vacuum table would be another way out or double sided tape. Just a few things that most definitely get you a better finish and a much nicer cutting sound with longer lasting tools.
Good luck and you must report back with more videos.
Cheers M
No, Little-Johnny, pomegranate is not a type of English stone.