maybe what isshin ment was that the hollow only fully raised its head and broke the spirit shackles in the byakuya fight?
as for urahara and the pit, I agree that was where the hollow was made a part of ichigo but actually that was bound to happen sooner or later, actually urahara gambled on ichigo awakening his own shinigami powers so he can hold it in check himself eventually.
If at the point where hichigo took over for the first time ichigo had not advanced as far with his shinigami powers ichigo would have been screwed. So in a way urahara laid the basis for that by bringing out his shikai.
then again all this might have merely been kubo forgetting about the whole pit incident
