I think my interpretation that "in accordance with its own constitutional requirements" refers to the decision to withdraw is supported by the ECJ decision that "The United Kingdom is free to revoke unilaterally thenotification of itsintention to withdraw from the EU. Such a revocation,
decided in accordance with its own national constitutional requirements..."
https://curia.europa.eu/jcms/upload/docs/application/pdf/2018-12/cp180191en.pdf
Implicitly, any withdrawal agreement must be done under the country's constiution (hence the Supreme Court supporting Miller that notice under Article 50 needed Parliament's authority rather than the PM's whim). Previous extensions have needed an Order in Council to change Exit Day, but under the new Act Parliament can require the PM to seek an extension. So, yes, it can be argued that the PM's unlawful refusal would frustrate the constitutional requirements that might have led to extension (or revocation). I'm just not sure how and when it would get to the ECJ so
de facto would usurp any
de jure.
I much prefer the scenario where Johnson gives the Supreme Court the undertaking not to prorogue Parliament again, so even if they find the current prorogation was lawful (even if he deceived the Queen) Parliament gets to vote for a second referendum, or simply to Revoke, and the EU says we'll take that as "in accordance with its own national constitutional requirements".