Over the years I have had 3 different double-sided proofing systems.
1) Our first was a SpinJet 1000. It was an accessory for the HP DesignJet 1000 series from TechSage that would automate flipping the sheet. It used a single printer. The first side would print from a roll, while printing the SpinJet would grab the leading edge of the sheet. Once the first side of the sheet was complete, the SpinJet would take the leading edge and reverse is back into the printer over the platen and then start imaging the second side.
2) The second was a DJet from Diginfo. It was two EPSON Stylus Pro 9800s stacked on top of one another, but facing opposite directions. The top printer would print the first side off of a roll, cut it and then drop it into a guide/hopper for the infeed of the bottom printer.
3) The third was an ImpoProof. It was two Canon printers in line with each other. The first printer printed the top side from a roll. This set-up did NOT cut the sheet from the roll after the first side printed. the "web" fed into the second printer for printing of the second side, then cut it from the web. This setup also had a camera that was used for from-to-back registration.
Each system had their strengths and weaknesses.