First of all ... should you be reporting this back to the dealer?
Did you see the table set up before you bought?
Was that table acceptable?
It's a pricey machine, to have a table that is going to cause problems for you.
Because of the size of the extended table, I am guessing that you bought the Bernina sit-down.
There are different tables available for it ... but your dealer may not be selling them.
The dealership near me has a beautiful table ... solid and very much like a dining room table!
Everything is very straight and smooth, that I would not foresee the problems that you have noted.
I would be very hesitant with any sort of a plastic film/sheeting.
It would be too easy for it to come free as you are FMQing and then you would have a mess!
Agree too, that contact plastic is probably not a good solution.
Within time it does wear out, and over those humps and hollows,
the plastic would crack/break and create roughness.
S16 sells a thin sheet (plastic? silicone?, at first glance like arborite, but not).
It fits over the top of your table to allow your quilt to slide, while filling in the gap where the machine is inserted in the table, with an opening at the needle area.
You might want to inquire what it is and perhaps you could buy the same at a home-supply store.
However, I still think you should be going back to your dealer and get them to solve the problem.