If you use the MFT as designed, the rail remains stationary and you move the fence to cut other angles, you'll only cut one groove in the surface. But it's your table to use how you please.
Cutting stuff that is lower/thinner than the fence requires placing the work on something sacrificial. You don't want to lift the work too high so I keep some 1/8", 1/4", and 3/8" scraps nearby. The 1/4 and 3/8 risers are MDF but anything flat and smooth is good.
Cheap is good too so you don't mind ripping the riser down so the clamp holes are uncovered. Pieces can be taped together with packing tape. The 3M heavy duty version doesn't leave it's adhesive behind.
One of my favorite materials is 1/8" thick melamine covered double tempered Masonite called "tile board" at Lowe's for about $10 for a 4'x8' sheet. It's flat, smooth, and cheap. Bright white on one side and dark brown on the other, which makes it useful for photography too. The white melamine side can be sanded with fine abrasive and then it accepts pencil marks beautifully.
Another I use it for is quick and dirty zero clearance covers on the table saw. Once the fence is set just lower the blade and tape a good sized piece of tile board over the blade insert. It can be waxed if needed.