Well, we actually do have a pretty good idea which general regions of the brain are responsible for which tasks, but that only applies to "normal" brains. Young individuals can get by reasonably well with a lot of damage or missing regions. Not necessarily true of older ones.
I know. In fact, adult brains seem to be
more plastic/adaptable than once thought.
However, the boy's case is unique in the respect that, generally, in cases of extreme brain plasticity and adaptation from damage, functions tend to shift from one hemisphere of the cerebral cortex / forebrain to the other. The cerebellum and pons (which control a host of processes such as respiration, coordination, eye movement, etc.) are not a part of the cortex. The cerebellum has lobes but not necessarily in the same way that the forebrain has complementary, hemispherical lobes.
In this boy's case, it's not that these structures are damaged on one side and their functions have shifted to their other hemisphere, they're simply not there at all (as far as can be seen). The entire structure of the cerebellum is non-existent (at least visually). They were there in the womb and then, well, "disappeared."
That's what, to me, makes this case fascinating. Hindbrain functions have completely shifted to the forebrain (at least, seemingly). It'd be like if you were born without a liver but somehow one of your kidneys performed all of the missing liver's functions. Well, not exactly, but you get my point.