Funny but I can see many reasons and we have the new Mac Pro as a prototype. Imagine a Mini using that tower box with the "CPU" card on one side of the devices and an option slot on the other, with the Apple option being a GPU card. Obviously the integrated heat sink isn't viable here but that just means conventional heat sinks are used. Done right there is plenty of room for the CPU heatsink, RAM and even the SSD on one side. The "tower" would have to be a bit taller but that is no big deal. Even if they had to put the SSD on the other side of the divider you still get a compact design with great cooling potential.
The reality is this, the electronics gets smaller every year. Haswell dramatically lowers power considering what you get in each chip and that only will become more dramatic in the future with the process shrinks to 14nm and much higher integration.
This pic says it all:
http://www.tekrevue.com/wp-content/uploads/2013/06/20130614_airportextremeac-10.jpg
Note too that the decider that separates the chassis into two parts is really an insert. As such it could be adjusted in a number of ways to accommodate the guts of a Mini. We have what is close to 3.75" square inches of floor space in an extrusion that can be as tall as Apple needs. The diagonal would allow for a PC board almost 5" wide.
If there isn't room in the base for a power supply, it could always be placed on the other side of the diagonal. I would prefer that space be allocated for a GPU card option though. In any event this is the perfect chassis for a Mini replacement effectively being a Mini Mac Pro from the cooling standpoint.