Rust could be from the pallets or wire used to hold the rock on the pallet. I would definitely rinse it off and then wet it periodically to see how it behaves. Ascorbic acid will remove iron stains from rocks or plaster.
Flaking and SWG are pretty much unrelated. It is a conspiracy theory that PBs use to avoid warranty claims. The stone is flaking now and hasn't ever been near a saltwater pool. We have some flag that flakes and some that doesn't after 5 swim seasons. We also have flaky flagstone on paths nowhere near the pool. Fortunately, the flaky flagstone in our coping has gotten better, not worse. For the most part it shed some layers and settled down. We have very little issue with it now. It is easy to tell which flagstone flakes and which doesn't just by looking at it.
So, I guess I could start a new conspiracy that installing flaky flagstone around my saltwater pool actually cured my flagstone issues.