As for the uA1, it's compact because one of it's main markets needs that size - bear in mind part of this is to replace use of CD32s with SX32 modules ;-)
As for IRQs, thats a given, even on MiniATX you can whack on a riser, they're not the devil's spawn, but a standard PCI compliant item.
Personally I find the idea of having an untra-compact base unit very appealing - I'm tired of hulking great (oversized) PC towers at work!