This is... a not entirely unforeseeable aspect of the tragedy of Brexit.
DEFRA, like for that matter every other gov't department both in the UK and in Europe, can't fully "prepare" for Brexit when no-one has the faintest idea of what, specifically, it's preparing for. And with negotiations still up in the air, and expected to come down to a traditional EU-style deadline-crushing intensive finale, no-one is going to know that until it's too late.
If they'd gone to the other extreme - creating contingency plans to cover every possible outcome of the negotiations - they'd have been (rightly) castigated for wasting hundreds of millions of pounds on consultants planning for things that were never going to happen.
The takeaway from this, apart from "let's shelve Brexit for at least ten years or so", is: don't have a referendum with a vague proposal. Negotiate and pass all the laws you need to first. Then the only question on the referendum paper is, "should these laws go into effect?".