When cutting the first side of the gantry I used the "traditional" hold down method of clamps and the like on the edges. That works ok when you have a much larger piece of alloy than the part you are cutting. In this case there isn't much spare in the height axis (left right as shown) and as you can see very little in the x axis (up/down in the below image). My clamping allowed for more vibration on the first cutting than I like so I changed how I went about the second side of the gantry.
For the second gantry, after flipping things in the software so that I was coming in from the other side I drilled out 4 m6 holes and countersank them.
This way the bolts (m6x40) were almost flush with the work piece. These bolts go straight through the plywood and connect with t-slot nuts in the alloy bed of the cnc. So there isn't much ability to use bolts that are too long for this application. Counter sinking the bolts helps on a machine with limited Z travel as using some non stubby drill bits really locks down the amount of free play and clearance you can get. The downside of this work holding is that you are left with 4 m6 holes that don't really need to be in the final product.
In this case it doesn't matter as I can use them and a new plate to mount one or two cameras on the back gantry facing forwards. I have found that the best vantage for CNC viewing is when not in the same room and looking at the video streams.
In future jobs I might move the countersunk bolts to the edge so they are not on the final work piece.
So now all I have to do is free this piece from the waste, tap a bunch of m5 holes, drill and tap 5 holes on 3 sides of the new gantry pieces and I'm getting close to loading it on.