Seewolf, that DOES answer the question to an extent.
If the parts between the casing and the PH were primed and painted with topsides paint and not antifouling, then they could in effect be almost any colour. That means that they could be dark on some boats, or light on others depending on what was available in the shipyard at the time. Or what colour the parts came from the various suppliers.
For instance, hi-pressure air lines or tanks might not necessarily be the same colour as the spare torpedo storage tanks, and neither might be the same colour as the air intake ducting or exhaust pipes.
In particular, it might be reasonable to think that some of the shut-off taps and valves would be bright red to be able to see them in an emergency or while working during refit. Underneath the deck the bright red wouldn't matter, since any enemy close enough to spot the colour between the decking would already have seen the boat.
I've often wondered about the colour of the hi-pressure air tanks in that regards since at least today, welders oxygen tanks are a royal blue while the acetylene tanks are sort of a moss green. (Or perhaps I have them reversed, I don't weld) In any case, it makes sense to be able to tell them apart easier.
Again, if that's the case, then it means that we could make these in-between parts more visible through the free-flow holes by using different colours. This would make them show up a little better in the dark.
Not that the colours would be vastly different. But if even some of the parts on top of the PH were the colour of the topsides (different shades of grey) and the air lines and tanks say a welding air blue, it would give them some definition in the dark.
Now, if only there was some way to find out for sure.