I started writing this post 24 hours ago so some of the things have already been said by now by the time I complete it, but anyway...
And that can easily be solved by displaying in a pack's information whether or not direct drop is allowed.
Which no-one is gonna read (I doubt you're gonna put it in big bold red letters on the title screen of a level pack), or even understand in case of players not aware of the behavior.
Ultimately it's not so much an issue to people who are aware of this thread and thus know this issue exists, but if you hand various level packs to someone not involved in the community, if they'd even test out the behaviour to see if it works, they'd then come to a conclusion that doesn't apply universally.
I don't see the point in comparing this to other weird mechanics Nepster mentioned; once you got these figured out, even if they are not intuitive, you can trust your findings.
You should just decide which physics you're gonna use and roll with it. Simon and I agree that having direct drop ('bad physics' -- Simon) is better than having inconsistent physics via an option. (For the record, Proxima doesn't agree.)
In the same vein there should be no other options affecting physics.
Options always tend to be a nice compromise solution and I'm not surprised at all that it ended up being a popular choice in the poll. But there's a difference between options for the player and options for the level designer that have an effect on the player (obviously UI options for the level designer in the editor are not an issue). While the former kind of option is something that the player might not even enounter, the latter kind of option has to be carefully considered.
There are levels out there that rely on this behaviour, some of which could not easily be adjusted to not rely on it - especially if the creator wishes to stay within the "traditional" options (those not so worried about this could often solve it via the use of updrafts).
If you want to stick to traditional options, use Lemmix. I don't get that rationale, if you don't want to use updrafts to fix your level, that's your problem. I'm highly not convinced that there are levels that need an elaborate fix to work, I'm happy to be proven otherwise with a concrete example. Is the sky set extensively used outside of the Lemmings Plus series?
Either way, levels requiring changes due to using the behaviour are easy to track down (you know the intended solution), while tracking down levels that require the assumption that the is no such mechanic is hard as you'd have to look for possible backroutes in each individually.