If this developed into a full-blown rumour that would be hilarious.
But yeah, really good theory, never really thought about it myself - although I've always assumed his Salamence saved him, and he got it fully evolved - he has Shelgon as he feels he needs to raise one from a Bagon to be a true Dragon master. Salamence can fly and use Hydro Pump, so could have easily saved him from a shipwreck. Plus it's big enough to make a mess of the insides (if rocks hadn't done that already).
Here's another idea though: Rayquaza saved him. When he says "I dedicate myself to the pokémon that saved me" he means how he's training dragons in tribute to Rayquaza.