Pokemon, what happened to you?

[Chaoxys]

I actually believed what Subomi stated on the reason of the gyaradoss colour was from the game or anime

I know it was. My point however is that if you were to look in the Lake of Rage long enough, you would eventually find a red gyarados that is not related to team rocket. So the one referred to in D/P/Pl could either be a wild shiny Gyarados, or a hint that Team Rocket evolved the Magikarp prior to the events of HG/SS.