I'd love to hear what part of the game does not make sense.
Are you really suggesting that the game would have been a better game if the player's party walks into the final dungeon, then promptly dies on the spot from severe BEW-poisoning followed by a "The end....sucker!!!!"? I'm probably misinterpreting things, or...
Perhaps, but figuring that Zio was merely conjuring a weak manifestation of Dark Force, I'd approximate his 'direct hit' version to be about the same (maybe weaker than, even) as the BEW emanating from the Garuberk Tower.
I think it's the opposite. To pull an analogy, Zio's BEW was like a wave of toxic waste being shot at something...physical constitution ceased to be a factor due to the sheer concentration of energy in the assault. The wave emanating from the Garuberk Tower was more like polluted air...potentially deadly, but people with a hardy constitution and resistence could avoid becoming ill for some time while being in the contaminated area due to the black energy concentration being much lower.
After all, the Profound Darkness' BEW is able to kill the inhabitants of Mile in fairly short order with a similar emanation of the BEW coming from The Edge.
That's simply because the black energy concentration in the wave coming from the hole south of Mile was many times higher than the wave coming from the Garuberk Tower. Instead of polluted air, think highly toxic air. The dose makes a big difference.
The real question is, how did Rudy/Chaz and company manage to not come down with any signs of illness (sure, the 'Rings of the Stars' protected them from PD's power, but the other Dark Force incarnations...they were just damned lucky I suppose ;p).
For the same reason there were still people on their feet in Meese. Some people are more resilient than others.