Dude, if you are going to go all-out on a case, that IR and Remote suck! ...and why do you need a VFD if you have a 7" touch-screen?
You want a USB-UIRT and a cool universal remote like the Logitech 880 or the Harman Kardon TC-30.
Volume is controlled by a reciever, not the PC. PC volume should be locked at max always (same for CarPCs with a Head-Unit). If you really want a knob, get a Griffen Powermate and you can glue it to the front of the case .
(BTW: I am currently building a system like this too: The first case you posted, HK TC-30, SnapStream /w PVR-500, Meedio, Girder /w USB-UIRT, 3x 200GB HDDs, DVD +/-RW DL, Logitech DiNovo Keyboard, etc., etc.)