The reason they didn’t do the lift compacting is there are 20+ pvc runs due to the infloor cleaning system and all of the vibrations a few feet above could affect it.

- I am fairly certain a pool pump gives off a constant vibration..
As mentioned above the only reason vibrations would cause a leak is if it is a weak joint to begin with. A proper solvent weld joint on scdl 40 pvc should be stronger than the pipe. We compact over pipes with lower ratings than scdl 40 all the time and compaction has never caused a leak. It does not look like they bedded the pipes in sand so I would be worried more about large chunks of clay or rocks being dumped from 5' above the pipes causing a leak than I would be worried about the accepted practice of compaction.
While we are on this topic... It is clear in the pics that the pool equipment was plumbed before the backfill was complete. When and how long did they pressure test all those pipes? I think it would have been wise to leave the pressure test going until the backfill was complete. You might want to ask the PB how they pressure test the pipes to make sure nothing got damaged in the backfill operation.
Since it’s a concrete walled pool they only over excavate approx 2ft, up to 3ft in some areas. He said they also connect the decking right into the pool walls with rebar.
As Jimmy said they are relying on the concrete to span the void. Which might work if it were only 2-3' but the pics clearly show there is more than that in some areas. Attaching the deck to the walls is not standard practice in my opinion.the deck will move with the frost and the walls will not. I think you would be hard pressed to find a engineer that would want them attached. There should be expansion joint between the wall and deck.
With that said, he told me to discuss with concrete guy next week and have them remove some of the dirt and they’ll backfill stone below the decking
I do not believe stone is a good idea at this point. In soils with poor drainage the stone will hold the water and saturate the surrounding material. This would work well to get things to settle if it were installed now and let sit over the winter, However it can also work against you after the pour if water finds its way into the stone. If you do add stone I would put in some drainage pipe out to daylight so the bottom of the stone bed can drain. The material that will most likely settle is lowest loose material so having stone on top will not help. It will just sink with the rest of the material.
I would recommend using the money you would spend on the stone to pay for removal and proper compaction of the original dig.
If you end up just trying to flood settle you should at least dig a small moat around the pool. Take the dirt you dig out and make a berm to contain the water in the entire dig area making sure of course the top of berm is well bellow the top of concrete so you do not flood the pool. If possible run some 4" flex drain pipe from your gutters into the moat. This will add a tremendous amount of water in a storm event and give it a proper flood settle.