Looks good, looks real good...
So I do something kinda similar, I'm using a secondary wasteboard on top of the one that came with the machine. I drilled it full of holes and put those threaded inserts into it, it works, but it always manages to irritate me in myriad ways. I've kinda been thinking about moving over to a T-slot board like this (except made from aluminum)
What I did, is I have a large selection of screws, in 1/4" increments, and I use those for work-holding, this generally avoids the tool hitting the clamps as they all sit much lower. I'm also using delrin or PVC for my clamps as it's a bit more rigid than the MDF/plywood. and I'm only using 3/8" thickness.
Over-all, I like your design, and may steal it.