Well, turned out the only way to get the GX4000 cart into place was to squeeze it between the SMS cart and manoeuvre it to the side. That meant I couldn't mount it on the case top layer, so instead, screwed a NES Toaster lid (it's about 1.5" and at a right angle), hot glued a piece of framing board onto it first. Then, placed the GX4000 board on top.
System works, as you see in the pic, and I have only about 1.5 cms headroom left, enough for the TurboGrafx!
One issue though, I wired the back of the SCART port on the GX4000 tapping just the RGB and C-Sync lines to my SCART connections, and I get a diagonally scrolling image. As you see, no shorts, and it works fine with a direct SCART cable connected. That means there must be an issue taking the signals off the GX4000's SCART connections. I'm going to have to see if the other RGB connection from the GX4000 works better, if not, work out what I can do to fix the issue.
Here is a pic of the cart connectors, the GX4000 and SMS ones, on the shelf. They are held in place by screws onto posts, so can be removed easily to allow removal of the console boards, as all the cart based systems are.
Need to experiment to get the GX4000 working properly in RGB!