It's a possibility, but it also could be a reference to Team Rocket's experiments in Gold/Silver/Crystal that screwed up the Lake of Rage (and thus created the Red Gyarados). Either way, it IS a nod to something.
FR/LG also makes a reference to Silver (someone in the Rocket Warehouse mentions Giovanni having a son with red hair, and we know by manga continuity that Silver is Giovanni's kid, so...)
Of course, D/P/Platinum in turn makes references upon references to the other games, so maybe they're just having fun.