Yeah, it happens when an operator doesn't have a failed regulator on-hand. It works, and gets the game back up and running, but it's not "correct". As you mentioned, the boards stay powered up even if you turn off main power for the game, since I'm assuming the power supply is plugged into the service outlet. But, in an arcade, that doesn't matter a whole lot, since the outlets are usually turned off instead of each individual game.

That's what I would do. But keep in mind, that might not be the only problem with the 5v circuit.

The big capacitors are very heavy since they stick out off the board quite a bit and it puts a major strain on the feedthroughs on the power driver board. The traces run on the top side to the big capacitors, through to the other side of the board and then to their designations. So very likely if you fixed the feedthroughs or ran wires on the back of the board to eliminate the top side traces, you could remove that non-factory power supply.

This is a common problem with the original power driver board.

Here is a thread I helped out with that talks/shows more about the damaged feedthroughs under the big capacitors. https://pinside.com/pinball/forum/topic/capcom-breakshot-dmd-voltage-trouble-shooting-also-lighting