Dario,
Zelkova roots are very vigorous. Screwing the wood on the bottom will prevent them from growing down. The force of the screw holding the trunk down will prevent them from growing down.
Had it just been placed on the bottom of the pot, the roots could grow down, and actually force the tree up when they hit the bottom.
I think next spring the tree should be barerooted again, and the base of the tree be examined, and a true bottom be established. This first year, just get it to grow, and survive the separation.
There is likely some trunk left on the bottom that should be removed. With fragile new roots, you don't want to mess with them TOO much. This will be an ongoing process: Exposing the bottom of the trunk, carve the new callous that forms, prune wayward roots, keeping the bottom flat, for a few years. Eventually, it will heal over.
Also, screwing the wood on makes it pretty stable. Which again is good since a tree blowing in the wind can disturb new roots.