I, like you, think that Gloucester is equal temperament. However, I was once told that it is not an easy organ to tune and there have been several tuners since Nicholson's took it over. If they have been of the old school, used their ears, and set the 12 notes up without reference to one of those digital tuner things then I expect they have all tuned in a variation on equal temperament. Would this account for what is now perceived to be an un-equal temperament?
That aside I was also told the sun has an effect as moves round from East to West and shines on the case and (even with the roof now unfortunately removed) can throw out the tuning. Before the recent rebuild domestic venetian blinds had been fitted on the East front behind the historic Harris front pipes (I kid you not) but whether they were re-instated by Nicholson at the time Downes scheme was amended I do not know. When I last heard, a year or so ago, the organ's tuner was a Lay Clerk at the Cathedral.
PJW