I found that putting the large case (standard μATX, for low noise) on a stand under the desk (carpet+dust considerations) with a small homemade wooden box for I

I found that putting the large case (standard μATX, for low noise) on a stand under the desk (carpet+dust considerations) with a small homemade wooden box for IO on top of the desk worked well. No reason to have the big box visible when you only interact with a percentage of it. Just like a power distribution board is in its own closet and you interact with it using power outlets, the desktop computer was away and I interacted with it using USB devices and the on button. The only reason to get near it is for maintenance. The on button is just two copper wires that need to make contact in order to boot the computer. You can use any old button from a store or make one yourself, or use a wireless one if your computer is really far away. The USB hub's case can be removed, and if you use the motherboard's internal audio chip you can find ready to use AUX extending cables for nothing. Of course if you don't want to make a custom IO box you can just use a regular USB hub and a remote.