Answer has been found, via Dave Barr.
Dave has another great article on BA that's going to be published on EliteFTS shortly, but I was lucky enough to get a sneak peak at it last night.
The short explanation of "why" beta alanine stimulates the parasympathetic nervous system (PNS) is this: it causes increases in GABA, an inhibitory neurotransmitter. Beta Alanine acts as a re-uptake inhibitor of GABA. This makes perfect sense why late night dosing is great, and why PWO is essential.
Think of it like this: A common class of prescription drugs for patients with depression are SSRIs - Selective Serotonin Reuptake Inhibitors. In people with depression, they often don't have enough circulating serotonin. SSRIs don't "make more", but they cause what serotonin they do have to stay in the synaptic gap longer before being take up by neural transporters. Same thing with BA and GABA, albeit transiently at the time of consumption.
Perhaps Dave will chime in on this also.