The only second votes ignored are those of people allocated their first choice. Leave people sometimes argue it splits their vote but it doesn't because if one of the Leave options came third and was eliminated the majority of the second choices which came into play would be for the other leave option.

The only disadvantage of two leave options to one remain would be for people who make a random choice from the options, which would advantage leave, but hopefully there would not be too many picking at random.

I don't think a series of binary ballots works very well: the campaigning alone sounds horrendously complicated.