When Theresa May wrote to Donald Tusk, the president of the European council, this week asking for a short extension to article 50 to 30 June, she will have known the request was likely to be rejected. But she at least knew she could avoid mass resignations from her cabinet.

The prime minister had vainly sought a similar delay, albeit without committing to holding European elections, at the last summit on 21 March, with the agreement of cabinet. She could be confident enough about the consequences at home of tabling such a request again.

But with the EU now appearing likely to reject her plea and deliver an extension of up to a year, ending either on 31 December or at the end of March 2020, the consequences are far from obvious this time – both domestically, given the potential shock in her party, and with regard to the EU-UK relationship and future trade negotiations.

One such wrinkle is the 21-month transition period – and the unfortunate fact that the extra period of membership will eat into those months thought vital to negotiating a comprehensive, all-singing, free trade deal that could both deliver frictionless trade and solve the problem of avoiding a hard border on the island of Ireland.

Article 126 of the withdrawal agreement lays out a clear end date for the transition, a period of time in which the UK effectively remains a member of the EU but without representation in any of the bloc’s decision-making institutions.

“There shall be a transition or implementation period, which shall start on the date of entry into force of this agreement and end on 31 December 2020,” the draft treaty says.

The 21-month duration of the transition period was not a UK government choice. It was decided on by the commission to tally with the end of the EU’s seven-year multi-annual financial framework (MFF). It made for a neat fit. Britain’s financial obligations were clear.

But by writing the end date into the withdrawal agreement, a deal the EU says it will not reopen, room for manoeuvre has been squeezed.

A Brexit delay until the end of March would leave the UK with a transition period of only nine months – hardly enough to negotiate much if the last two-and-a-bit years of onerous talks is anything to go by.

If the UK wanted to extend the transition “by up to one or two years” as foreseen in the withdrawal agreement, a decision would need to be taken in July 2020 – four months into the transition period – by the joint committee overseeing the implementation and application of the withdrawal agreement.

And if the UK did not extend the transition period, the Irish protocol, or Irish backstop, would be the legal default nine months after the negotiations proper on the future relationship had begun. From 1 January 2021, the EU and the UK would share a single customs territory, and Northern Ireland would stay in much of the EU’s single market acquis.

“We shall just have to negotiate quicker,” said one senior EU diplomat about the unforeseen consequence. In reality, at some point later this year there will have to be a reckoning with this problem – and it will involve extra costs on the £39bn divorce bill.

The end date to the transition period would need to be revised in the withdrawal agreement. And, as at least some of the newly framed transition period will be outside the 2014-2021 MFF period, the UK would, in such circumstances, need to make significant Norway-style payments to the EU for that extra time.

Brexit has been described as one of the most complicated negotiations in history. It just got a little tougher.