Jenova's entire head would not fit into that small box. It had to have been pretty battered, and the whole head probably was not in there. Just a chunk of it.

Although now that I think about it, when Kadaj absorbed Jenova's remains in AC it looked like he was actually holding on to something before he shoved it into his chest. There probably was a pretty good chunk of its head still intact then. Big enough for Kadaj to hold and small enough to fit in the box anyway. The rest was probably liquid.