"The real problem is that the Equipment Capability customer in town started with the assumption that STOVL was the way forward and that view never really changed."
True, and a classic example of an assumption being undermined by facts, but so slowly that it was not perceived until so late in the game that, barring catastrophe, it would not be changed.
Pre-JSF, UK sea-based air was clearly welded to the CVS. Even the JAST/JSF planning stage assumed that the jet would arrive while the CVS still had some lifetime left (remember little folding wingtips on the LMT PWSC B-model?) and that the follow-on would be a small STOVL carrier.
At the same time, STOVL was UK plc's ticket on to the JSF program and by 1994-96 it was pretty clear that JSF was the closest the UK would come to building a stealth fighter.
I think it was 2003 when I was briefed on the 65000 ton CVF, so in the meantime three key discoveries had been made about sea-based fast-jet air, on a system basis: Ship size was driven by aircraft numbers, and catapult/arrest vs STOVL was not a big factor; steel was cheap; personnel was the cost driver.
But by that time nobody wanted to throw anything in the path of the JSF train - indeed, I think it was still predicted to enter service in 2010, and the B was projected to beat bring-back requirements...