As an official, one problem I've always struggled with is with the wizard modes on World Cup Soccer and Tales of the Arabian Nights.
Both of those machines have unlimited ball saves for a certain amount of time. When a ball drains, it is re-served to the plunger lane immediately.
Is leaving a ball in the plunger lane in this circumstance disallowed? Note that the stuck ball rule also includes a line which reads...
A stuck ball during multiball often represents a significant beneficial malfunction, and intentionally taking advantage may result in a penalty.
In the WCS and TOTAN examples, the ball in the plunger lane arguably does not represent a beneficial malfunction. (In fact, the rulesheet for TOTAN states that leaving a ball in the plunger lane makes the Genie pull the bottle to his side faster, so it is probably a disadvantage.)
We used WCS in City Champ two years ago. As head official, I discussed it with our state commissioner and I decided to announce ahead of time (and put a sign on the machine) that it was explicitly allowed to leave a ball in the plunger lane on WCS in the Los Angeles Wizard Mode (partially because it was unclear whether there was an advantage, but also because as an official, I didn't particularly want to be forced to DQ a player who would have gotten to the wizard mode in tournament on a machine which was set up so extremely difficultly).
I've never been sure whether this was the right move or not. Announcing it ahead of time leveled the playing field at least, though.