On our 5x12 machine at work, we cut .003" into the spoilboard, and resurface it when small parts start to move.
The curling is due to changes in humidity.
If the corners are curling up, just flip the MDF over, and it should flatten out easier.
If you have enough vacuum, it should remain very flat with vacuum applied.
As soft rubber seal in a channel around the perimeter may help to pull it down better.