That's what is odd about some of the Midways, they are NOT separate. Where you would normally see the light fixture and such on it's own output somewhere, Midway has them tied together.
I just worked on a converted Midway cab the other day and it was the same way, the only isolated winding went to both the light fixture AND the monitor. i wanted to verify it myself before I wired up the monitor. There are four wires, but the are indeed tied together. (one isolated output split two ways)
Strange then that they even bother having the two sets of output wires. The wiring diagram calls for the monitor to be on its own set of wires, and the marquee light and DC supply to be fed from the others. This would be what you'd expect for two isolated output windings. However, most cabinets were not wired that way. They usually put the monitor and marquee light together. Of course, none of that matters if the outputs are actually just the same winding internally.
The reason this works is that the DC supply is also isolating, and the marquee fixture can just float to whatever it wants to. This means there's no ground loop from the game to the monitor via DC ground. The fact that the single output winding is still isolated from the AC mains means that there's generally no shock hazard. Still not the way I'd do it.
Actually, strictly speaking, the isolation transformer for the monitor isn't necessary at all in a system with an isolating DC supply if you don't mind every single wire in the game being a major shock hazard.

Of course, it's very, very wise to include it precisely so that this isn't the case. A trivial loose wire could result in your joystick or coin door shocking users (this is one reason why external metal surfaces are grounded on cabinets).
Once you reference the DC outputs to somewhere (e.g. by tying them to earth ground, which I think Midway usually did), you absolutely 100% NEED that isolation transformer, though (otherwise you have a ground loop via the monitor and AC neutral back to the panel). Note that PCs do always tie their DC ground to earth ground, so this is always the case if you're using a PC.
Don't you just love the concept of "ground"?
