And this major flaw wasn’t discovered during the many testing of this cropduster
Did you notice the word “temporarily”? :-)
It's not a major flaw, it's very minor. Most fighters don't even have a system like this and they manage not to blow up. Not flying through thunderstorms is pretty much instinctive to any pilot anyways, telling one to not fly near a thunderstorm is like telling a chef not to cut himself while chopping vegetables. The engineers will fix it and life will go on, I'm gonna go out on a limb and predict that no F-35's will blow up because their nitrogen generating systems weren't working before then.
As for why not use a pressurized nitrogen tank? They add weight and have to be refilled which adds another unneeded layer of maintenance when they're on the ground. A self contained automatic system is much preferable.
This article is typical media BS of making a mountain out of a molehill. It's much ado about nothing designed to get the armchair aviation experts all worked up.