I wouldn’t take any of the baseboard material away, I went the other way and bolted mine down to the bench it lives on to improve the rigidity and get rid of some unwanted deflection.
Increased Z travel is a double edged sword, it can increase issues with bit chatter and spindle deflection as you move further away from the X rail by increasing the leverage.
As Will says, threaded inserts are a good idea, I started with T tracks between my extra spoilboard strips and thought that would be great. It wasn’t, I was constantly trying to figure out how to lay out the workpiece so I could reach it from the T track clamps, they’re good, but not enough on their own.
I finally added a grid of 6mm threaded inserts to bolt extra clamps in, where I actually want a clamp, they’re on 100mm centres, between the T tracks.
I also had the Shapeoko mill a grid of 10.2mm holes in the spoilboard in which I can put little 10mm Aluminium rod dowels to help me align the stock on the machine, which saves a lot of effort getting stock squared with the machine or re-zero-ing when making multiple pieces
