He does claim that a straight-classed dual-wielding rogue is fairly bad at damage. They're the second-worst combat class if you don't multiclass (and rogues at least can get a significant boost if they do multiclass; monks really don't have a way to do this, short of ignoring most of their monk abilities). Reasonable people can disagree about whether the non-combat abilities they get make up for that, but if monks are slightly behind rogues in combat and also don't have rogues' non-combat features, what are they bringing to the table?
Agreed. The analysis I did assumed they used all their ki on Flurry of Blows, so for that damage level, they can't use stunning strike at all, but yes, at higher levels they can flurry every turn and make stun attempts sometimes. But also their direct damage potential falls even further behind at higher levels, so the value they get from stun would need to be higher to close the gap.
You're skilled at quantitative analysis; why don't you take a crack at it? It'd be a useful contribution to try to put everything the monk does together in some common units... But then once you've done that, I'd suggest doing the same analysis for a warlock that spams Hypnotic Pattern / Synaptic Static and then pew pews (they won't have Hex up, so they will fall below the direct damage baseline, but that's fine, since they're bringing other things to the table), as well as for a Battlemaster archer using Menacing Attack, say, or a Ranger supplementing their weapon damage with conjured animals.