I sometimes like to use one box at a time, and sometimes like to use multiple together. I find keeping them all together doesn’t interfere with me isolating them.
The one thing I’d really recommend is focusing on ergonomics. Stuff can Look great, but if it isn’t easy and comfortable to access, you likely won’t use it. If you have a spot where you want to build out your custom interface known, sit down in front of it in a chair and imagine the height you’d want your Matriarch keybed to be, imagine reaching over it to tweak your MnM. What angle do you want the knobs to be? All that stuff should lead how you set it up. You can make the housing as aesthetic as you want, but if you lead from function and comfort, you’ll really enjoy your gear a lot more.
My setup is in kind of an advanced prototype at this stage…I knew I wanted the faceplates for my Boog, Digis, and REV2 aligned, so I built this test setup by hacking an IKEA desk and sawing some plywood…longer term I’d like to build out a proper CNC mill file for an entire desk, with better cable management. But for sure having my gear set up so it’s easy for me to mess with everything makes it all so much more playable and fun.