Generally a referendum will never occur with three options on the paper and the top one winning.

I'm unaware of any electoral system that uses that form of referendum. A couple of years back, I read a terribly dull and dense book about the evolution of electoral systems... turns out the majority of the different voting systems / democratic processes were developed in European monasteries in the Middle Ages who saw the ability to achieve "perfect representation" when choosing internal positions as getting "closer to God".

Actually fairly fascinating stuff... but tough to write an engaging book on!

All of which is a tangential way of saying that a referendum with more than two options is almost certain to be run in two stages.

EITHER it will be Option A:
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Referendum 1: "Leave or Remain".

If "Remain" -> done.

If "Leave" -> a second referendum "Deal or No Deal"

OR MORE LIKELY it will be Option B:
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Referendum 1: "3, 4 (or more) options"

Referendum 2: run off between the top two.

Option B is by far the most common way - globally - to deal with a referendum with 3+ options. But Option A is used occasionally.

We shall see...