I sometimes think that maybe the supercomputer is made with reverse engineered alien technology. That maybe Franz Hopper got his hands on a fallen alien space craft, studied it's technology and perhaps used it to make the supercomputer. After all most of the rooms in the cartoons were rotunda while the rest of the factory on the surface were of regular abandoned architec. It just seems too impossible for a human genius as Franz Hopper to make a machine that virtualize organic matter and doubles as a time machine no matter how intelligent unless they had the technology to study at first hand.
It's my own headcanon but what do you think? Maybe even XANA is more of an alien/human program gone wrong? Be interesting on it's personal oppinions on the matter of it's parentage.
Time Reversion could of been part of the spacecrafts engine used for travelling great distances. So to speak the craft was able to arrive at it's destinations before it was even there.
The spacecraft could of been the size of the average rooms under the Factory, I can imagine the center of the craft with the supercomputer doubling as the Lab and can have Scanners around the walls. The aliens created virtualization so that they can create artificial environments for themselves as well as control the spacecraft from whatever they had as Towers, if they needed such things, perhaps commanding the ship directly from the virtual dimension in the ship.
When the spacecraft crashed to Earth the ship was damaged. The ship went into Franz Hopper and Tyron's possession. (Either Franz found it or MIB gave it to them for the Carthage project) and made the supercomputer.
I suspect that the aliens were killed and erased completely when there ship fell. the impact damaged the machine and destroyed the CPU of the supercomputer. While they were in it, erasing everything such as how the spacecraft functions as well as who the aliens were and there culture or intentions making them a complete mystery.
This is all my headcanon on how Franz Hopper made the supercomputer.