The idea is to allow you to cut all the way through the stock material and into the spoil board without being able to hit the t-track and damage your end mill.
You could still damage your mill on the clamps but I’m hoping to able to use 3D printed clamps.
Just because you have T track it doesn’t mean that’s the only way you will secure your work. You may want to use tape/ super glue or you may want to just screw down the wood to the spoil board. You also want the top of the MDF flat. You could clamp the ends of the spoil board but the center could bow up, either right off or down the road (MDF loves to swell with moisture), that could cause you issues while trying to flatten the MDF.
I used 2 layers of 5/8" MDF. I applied glue to the MDF layers and screwed them down to 3/4" plywood. I used a countersink bit to sink the heads of the screws almost completely through the top layer of MDF to give me lots of depth for surfacing.
I went a slightly different route - I used 2 3/4" sheets of MDF, with the intent that the bottom piece is permanent, and the top piece is fully replaceable:
This picture is before I had anything glued down - the clamp “squeezes” the MDF top, instead of pulling up on the t-track. Need a little bit longer t-bolt to make this work, but it’s been working well for me so far.
Response to a different question: if you have t track across the front and back I would set it away from the ends of the other tracks else you won’t get your clamps in. Also leave room at the ends of these t tracks from the y rails for the same reason.
I plan on having clamps all around, I just haven’t decided how to cut them for the front and back. I ordered 36 feet of track so I should have some room to play around with the front and rear design.