I have wondered this myself, since I too have a A4000D -- although mine is a HighFlyer expansion case for my Toaster/Flyer system.
The Mirage tower case from Elbox looks really nice, but there are going to be some problems when it comes to my Toaster/Flyer system. The Flyer has 3 SCSI chains (2 video, 1 audio). In a normal A4000D, those cables have to go out the back where an expansion card would sit. Now the Highflyer case has this solved, because it has 3 slots in the case specifically for the SCSI cables going out. It's very nice. The one thing that I do NOT like about this case is that if I wish to upgrade my Amiga (such as 3.1 ROMS and add 3.9 OS or add a better accelerator card), I will literally have to tear down the entire case just to get to the motherboard. A real pain. If it was inside of a tower case, it wouldn't be so bad.
If the Mirage tower case was a full size case, then it would work pretty well for me. It would have room to put some Flyer drives. It's half height though. Not as much space as I would like, and I already have a "hard drive only" case for my Flyer drives.
So, I too have been wondering the same thing you are. How can we put an A4000D motherboard in a full tower PC case? I think we would have to modify the case with a sodering iron and drilling tools in order to screw the motherboard in properly so that it aligns with the expansion slots on the back of the case. You'd also have to cut out parts on the back of the case for the monitor, serial, parallel, etc connections. In short, it sounds like a big mess. But people out there have done it.
I've seen some really nice PC towers that have built in fans that look like it would keep a Toaster/Flyer system really cool. Plus, I would have room to put some Flyer drives in there.
Hopefully some Amigans out there who have done such a thing can enlighten us on the work involved in altering a PC case to fit an Amiga motherboard.