Although I think we ought to remain, I do see that a referendum WILL be complex.
If remain was to win the first question, then that's simple enough. Socially divisive but fairly clear.
Presumably, anyone who voted remain would also be able to vote for their 'least worst' leave option - although I suspect some might find it hard to put a cross in any of those boxes.
If leave was to win the first question, then if there are multiple 'indicative' options (let's take your three as examples) then each might get roughly a third of the vote. So if the (just selecting one at random) May's Deal got 35% and the others 33% and 32%, would MPs be bound to vote that through on a quite small minority win? Of course, the more options you have the more the vote will be split.
I'm not convinced the result (if leave won) would make things much clearer as to *how* we are going to leave. Which of course was the problem in the first place!
I would suggest that you can only answer the 2nd part of Leave if you have answered Leave in the 1st question. It would be far clearer than the original referendum what Leave actually represented. As the 2nd Referendum would be breaking the impasse we find ourselves in then by giving clear options (Remain and Leave) you meet that need. The Leave options weren't definitive, just examples and can be less so can be only 2 options if so wanted (clearly No Deal would be one).
With the Parliamentary impasse then I think it is pretty clear that any Referendum would have to have very specific options for Remain/Leave as the original Referendum question has proven to be a very poor question, being too simplistic for a complicated situation. I think any situation/decision is going to upset people now whatever Parliament does but at least a clear answer would be given.
I don't think the question really is that complicated but the surrounding situation will be, no doubt based on what has gone on. As said whatever happens now, due to the way this Govt and May has handled the process, there will be unhappy people at the end whether they be Remainers/Brexiteers or both.
I don't think we'll get a Referendum anyway. Should Parliament end up wrestling control of the Brexit process then I think we'll end up with something like EFTA. If May keeps control then I reckon a no deal is still likely due to her tunnel vision on her own deal and punishing* Parliament for not voting it through.
*Based on her actions so far I believe she would be that vindictive.