The size of the case makes general installation a little unwieldy, especially when turning it on its side to install the primary motherboard. Being able to remove the back I/O panel completely makes installation much easier, as you can avoid that tricky, slightly diagonal mounting of most motherboards, as you have to get the I/O ports through the panel at the same time as aligning the board to the mounting screws. This way, you can mount the board first and then refit the back panel over the board - much easier.
The vertical size of the case means that the primary motherboard is much further than normal from the optical and hard drives, so standard IDE/SATA cabling probably won't reach. The case ships with an extra-long dual-channel IDE cable and SATA cable, but that's only good for one hard drive. If your system connects to multiple drives then you'll probably need to purchase some more extra-long cables.
One distinct advantage of the Mozart TX's size is that it tends to eliminate the problem of internal cable clutter. There's a lot of room in between the drive bays and the rear of the case, so cables don't tend to bunch up and restrict airflow. It also provides lots of room to work with. Additionally, there are a number of access points cut into the mounting plate for the primary motherboard through which you can feed cables from the PSU positioned directly behind it. PSU cabling tends to be a problem at the top of most standard cases, and it's nice to have this problem minimised.
With any secondary system drawing its power from the drive bay PSU, you'd want to install the PSU in the bottom-most 5.25" drive bay. Based on a mini-ITX format, the secondary system really doesn't cause that much extra clutter, but you'd really want to install the extra 12cm and 8cm case fans in this section to reduce overall heat buildup.