Wasn't he? I don't see any reason FFVII!Cloud wouldn't have been exactly where he was supposed to be when FMA!Cloud was bamfed into the 'verse. That would leave one Cloud having been Hojofied, and one Cloud in the process of being Hojofied. Two horrors for the price of one Hojo!

Seeing as Tifa has just be carted off to Midgar by Zangan, and the rubble of Nibelheim is still smoldering (unbeknownst to the general populace, but knowst to us), the potential exists for all kinds of things to happen.