DOSBOX: Don't change certain settings to gain an unfair advantage, cycles, for example.

This is entirely fair, but what is the "unchanged" setting for cycles? The GOG version comes with a .conf of "cycles=fixed 8000", and I suspect that's a common use case: anyone owning an original copy, however, would likely install DOSBox manually and therefore have a default .conf of "cycles=auto" (which should result in a fixed 3000). So there's already a disconnect between naive runners.

The cycle setting (others can matter though very few ever do for timing/playability) is always going to be arbitrary, whether technical or aesthetic. Most games don't throttle their speed appropriately, M&M3 included, so it often comes down to what runners find necessary and/or sufficient. My own run from a few years back set cycles to fixed 20000: according to the description, "The cycles are to keep the game at a steady but brisk pace, allowing area transitions to occur quickly." (To be clear, I'm not here to argue whether my choice is better, and have no intentions of forcing a different-cycled run into the leaderboard.) By contrast, my Swords of Xeen run set max cycles because of the continuous saving/loading, which crashes way more often without it (though at least in this case, the GOG .conf also coincides here).

Regardless of what is chosen, I recommend clearly stating settings necessary for a consistent leaderboard. The GOG standard is reasonable here, but I've used DOSBox with many games and can tell you GOG doesn't always come up with settings I consider good for even a casual experience. Their settings are no less arbitrary than others that could make the speedrun more enjoyable to play.