It all boils down to a lack of protection in the middle. With no Stones, Rodri is on his own, with no KDB, Rodri pushes up and leaves a massive gap behind him. With Walker and Gvardiol having permission to go forward, it essentially leaves 2 defenders on the counter. It didn't happen in the 3-2-4-1 formation, because there was clear demarcation of roles. The back 5 defended, that was mostly it, and it worked.
Personally, I don't understand why Bernardo isn't positioned right next to Rodri and told to control the game, we know he can do it. He did it when KDB was out, instead, he's creating overloads on the wings and leaving us light in the middle.