k here's what it was to me: you kill hojo in 7, but he was obviously working on his plan before cloud and co. defeated him. in the beginning of dirge of cerberus, i dont think that vincent's actually seeing hojo, he's just freaking out since hojo was such a big part of vincent's darkness. but it's these projections of will and self that litter the 7 series like: you never actually see sephiroth in 7 until after cloud brings him the black materia - every time you saw him before it was just a projection of his will through jenova's body parts. i think something like this occured with hojo, since im sure he probably already started uploading his mnenomic data into the world database before you fought him in 7. make any sense? sorry i have it in my head but i guess i kinda suck at explaining.