Single transferable vote. Although there is only one remain option the first votes for the least liked option will go on to their next preference and so on, it would almost certainly come down to remain v the most popular leave option, which would be fair.My initial thought was along these lines. But I've since been convinced that finding option for the second referendum will be difficult. In your example there is only 1 in 4 remain options. Surely this bill would be hard to get everyone to agree on?
Look at this way, if there is merely a confirmatory vote then Farage's lot will say people only had a choice between crap remain and a crap deal, so the vote didn't count. Put no deal in as an option and they'd get what, 10%?, they would lose anyway, and would that not be a good thing?