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It appears to be unequivocal (them's the rules) if controversial (a lot of people don't like it) that for a bill that's passed both houses to pass into law it then needs Royal Assent from the Queen & by constitutional convention the Queen always follows ministerial advice (the PM's) on this.
It seems then that should the PM wish to & be willing to do so he can prevent the new Brexit delay bill from ever becoming law for as long as he is PM.
Is this correct?
The answer to your question is "possibly". There is even precedent for the government advising the Queen to withhold assent, although the nearest one is pretty old (from Wikipedia).
The last bill that was refused assent by the sovereign (on the advice of ministers) was the Scottish Militia Bill during Queen Anne's reign in 1708.
Additionally note the news regarding the Benn bill:
The gaining of Royal Assent for the bill was a requirement that Labour leader Jeremy Corbyn said his party would need before it considered backing Mr Johnson's call for a general election.
And in response to some comments: it seems there's academic controversy whether the Queen would have to follow the advice of ministers in such a controversial matter. On one hand...
Rodney Brazier, professor of constitutional law at Manchester University, argued that it would be unconstitutional for the Queen to refuse to follow the advice of her ministers.
Ultimately, he said, the constitution dictated that the monarch must do what ministers advised her to do.
“Few actions more dangerous to the perceived and vital political neutrality of constitutional monarchy could be imagined,” Professor Brazier wrote, “than the Queen rejecting the government’s advice.”
He added that “the convention that the Queen acts on ministerial advice is based in democracy”.
On the other hand...
Those who argue that the Queen should accept the advice of her Ministers do not explain at any length why they adopt this interpretation of the convention. Perhaps the best explanation of their understanding is that they group the convention on royal assent along with the rest of the conventions surrounding the prerogative powers. Practically all of the Queen’s prerogative powers are now exercised on the advice of Ministers, normally the Prime Minister. The prerogative can be used to appoint ministers, declare war, annex territory, sign treaties, and many other things besides. That the Queen no longer has any discretion about the exercise of these powers is important because it upholds democratic government. Ministers are accountable to Parliament and, ultimately, to the electorate, for the ways they use these powers. In the words of Walter Bagehot , a republic has insinuated itself beneath the folds of a monarchy.
But does this reason justify the inclusion of royal assent within the group of prerogative powers that are exercised on ministerial advice? It is hard to see that it does. Now the convention is operating against democratic values, rather than upholding them. Rather than supporting parliamentary government, it would undermine it. The point of the convention on royal assent is to uphold the primacy of the democratic element of the constitution in the making of law. But just as it would be undemocratic to allow one person – the Monarch – to veto legislation, so too it would be undemocratic to give this power to the Prime Minister. In short, when presented with a bill that has passed through Parliament in a proper manner, the duty of the Monarch is to give assent – irrespective of the advice of her Ministers. There is no room for discretion. On its best interpretation, this is what the convention requires: if the Monarch were to accept the advice of her Prime Minister on this issue, she would be acting unconstitutionally.
It is convention that the Queen normally acts on the advice of her Ministers - unless there is more specific convention that requires her to do otherwise.
In this context, the more specific convention is that the Queen grants Royal Assent to a Bill passed by both Houses of Parliament. That convention is superior to the convention that she follow the advice of her Ministers. It has been more than three centuries since a monarch refused Royal Assent.
When bills, either public or private, or Church of England Measures (on which see paras 31.46 –31.49 ), have been finally agreed to by both Houses, they await only the Royal Assent to be declared to Parliament to give them, as Lord Chief Justice Hale says, ‘the complement and perfection of a law’,1 and assent must be forthcoming.
https://erskinemay.parliament.uk/section/5552/royal-assent/
But that is Royal Assent - there is also Queen's Consent.
Queen's Consent may come into play if the Bill would significantly affect the 'prerogative powers', e.g. the power to agree international treaties, and there has been some debate about this with regard to the recent Brexit delay bill.
