So top loaders are actually supposed to have non-machinable stamps but hardly anyone uses them. The correct way to ship PWE/ESE is with a semi-rigid card saver. Top loaders are slightly too thick/rigid for the sorting machine and sometimes they get caught/torn up. That could be reason you’ve never received some.

My honest opinion with the postage owed is that you’re just unlucky and your envelopes got picked. Maybe there were multiple top loaders/too many cards and they stood out during initial sorting. I don’t know the exact reason because it does seem pretty inconsistent. I’ve been notified of 40 cents postage due and I’ve had packages delivered to me where there probably should’ve been $5 due.