The article doesn't convey the complexity very well.
Destiny keeps PvP and PvE separate. For PvP, it's traditional PvP. But for PvE, there are multiple worlds made up of interconnected regions, but because of processing limitations (even if it's MMO, it's still an FPS), the sub-regions are individual instances. So you need seamless transitioning between regions, while having to find you a populated instance every time you cross a region boundary. Oftentimes you will be doing a 20-30 minute activity that has to cross multiple instance boundaries, so your actual quest state has to persist separately from the physics simulation. If you take their design of the game as a given, then yeah, that's a bit more complex than most MMORPG's.
It's not really about matchmaking. PvP has explicit matchmaking, and in PvE lagging hit registration is generally inconsequential because it's not a competition. It's more about the fact that Bungie tried to work around the problem above using P2P servers.
The problem arises when PvP is still handled in a P2P-ish way and you have hit registration problems. On a quick read, I'm not sure I fully understand it though, because if the physics server is dedicated, then why are there still hit registration problems?