I think it's a combination of different facts that create this impression. After the explanations given in the latest update i believe the size is accurate.
First of all, aircrew inside bombers seem just right and correctly to scale.
Second, people who have read history books/wartime memoirs from pilots stated that all too often a piece of text desscribes how the pilots lowered their adjustable seats before entering combat, in order to align their line of sight with the gunsights but also in order to have more of their body encase within the harder parts of the airframe (the fuselage) and not sticking out at the height of the vulnerable canopy. In fact, there have been documented cases of pilots ducking as low as they could during straffing runs, in order to protect themselves by placing as much of their body as possible behind the engine.
Third, in this weeks update thread a wartime photo has been posted showing a pilot's head extending even above the open canopy. He couldn't have flown in that position, so his seat is either set high, he's standing semi-upright in the cockpit, he's taller than usual or a combination of the above. There was also a real-life photo posted from one of the members where his nephes sits inside a restored hurricane. The guys is said to be 6 feet tall and his head barely extends above the side walls of the cockpit.
Combining all these, it's my assumption that pilots generally adjusted their seats high for taxi and take off to help with visibility, maybe leaving it there during cruise as well to help with situational awareness and visibility during formation flying.
These planes were not only taildraggers, but many of them also had massive cowlings compared to light and general aviation planes that people fly today. I guess that if you need to lift yourself from the seat during taxi to maintain visibility in a piper cub, you'd need to lift the entire seat a couple of notches in a spitfire or 109 since they sport a much longer cowling.
During combat, they lowered their seats to keep their body protected and align their heads with the gunsight.
If this is correct, then the reason that most modern photos from airshow and restored warbirds show pilots on the high position is simple...they don't need to keep their eyes on the gunsight and nobody's going to shoot at them, so they opt to adjust the seat to a high position for better visibility and they seem bigger as a result