At first, I thought the depth of the pit probably includes the 3mm dome skin. But that's not correct either as the other back wall details we know to be correct don't touch the armour plating.
These are the only photos I have of the back wall. You can see the Hurricane magneto wiring harness to the right and a couple of 'blocks' to its left. Then the Centurion brace poking down to the armour plating, then everything else is obscured. I believe the height of the pit is correct because the Pay Hauler frame, the wiring harness, and that 'pipe' to the far left, all terminate at what would be the top (bottom?) of the pit where it attaches to the dome skin.
I think the two options to consider are that the 'Centurion brace' is sitting on something else about 3mm tall. Or, and this is unlikely, it is not from the Centurion kit at all, but something else. Something about 3mm taller.
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In this second photo, you can see there's a round/cylinder just to the left of the Centurion brace that I believe is part of the Airfix ME-109 that you found. Which, given that detail's position, maybe that whole part sits up higher in the pit?
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For the cut down barrel, this is how I have done mine. The reason I chose this route is because the 'raised' portion of the McLaren part isn't long enough. Mine is probably still not right. I cut it purposefully oversized slightly (the larger diameter area is still a bit too long) so I can still make small adjustments. But I think once the lengths are correct it certainly looks correct. I make no claims that's how ILM did it, but I don't think it's the McLaren part either. But as you say, the remainder of the barrel is used in other areas. So who knows, maybe I got it right by accident.
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Anyway, I look forward to seeing what you discover for the remainder of the back wall.