I know your grasping for answers but I think the whole idea that a 1" PVC pipe behind a light niche is eating up all your chlorine is not what's happening. My light fixture doesn't have a seal there either. It was built like 26 years ago so maybe it wasn't code then. Anyways just think about it. Even if there is a lot of algae in the pipe I don't think it is able to just flow out into your pool the same as the pool water with chlorine is going to have trouble flowing up into the light niche. And if your really worried about it you joked about the bubble gum idea but there is some stuff at Home Depot that is a two part putty usually white with a green core and you squish is all together and you can place it and it will cure underwater. I used to use it glue coral underwater inside a saltwater tank.
I do agree that they should focus on the SLAM, but I also think that their PB did a short cut job on a NEW pool that the Nelson's laid out tens of thousands of dollars for. They have every right to go at them to bring the light niche back to code.
I also think that sealing the pool from a source of stagnant water is important...no good can come from 80ft of stagnant water which, if you do the math, is roughly 3.3 gallons of water in that section of tube.
I also liked your idea of the underwater putty as I thought of that too. However, I would be concerned doing any kind of permanent sealing material as it will make any future work on the light wiring very difficult. Perhaps something as simple as a rubber stopper with holes drilled in it and sliced down the middle might work just as well.
This whole saga makes me think of how they do underwater repairs of bridge towers - caissons! Too bad there isn't a simple caisson that could be constructed to fit in a water-tight fashion around the lighting niche that would allow you to pump out just a small amount of water and allow you to work on it without having to drain 18" to 20" of water off your pool.....I'll have to start writing up a patent