This is an interesting topic, and one we discussed quite a bit as Pirate was first ramping up: the two worlds, sadly, cannot directly touch (that's a sheer impossibility form a technical standpoint) and we didn't want the story of one to become dependent on the story of another - it would constrain either or both games when coming up with where to go or what to do next. So we've been content to let the stories run in parallel, assuming that the Wizards don't pay much attention to what's going on in the conventional world of maritime geopolitics (spiropolotics?) and, conversely, that the doings of wizards and all their card-based magic was obscured from what pirates were doing.
But we did go out of our way to make sure that our story stuff in Pirate didn't contradict Wizard's timeline. I guess I'm going to have to go back and re-write that Aztecosaur dialogue: they have visions of the doom that Morganth would unleash on Azteca in the future, so they left.
Marleybone and Mooshu is where our stories get closest. I'd love for the Marleybonean/Armada war to have echoes in Marleybone Wizard content, but that's simply time gone by - when Wizard's Marelybone content was written the Armada (and Pirate101 itself) hadn't been conceived of yet. So we put Marleybone City "over there," at the edge of view. Threatened by the war but not yet embroiled in it.
And who says Merle doesn't know about El Dorado? There was a special Ninja Pig giveaway promotion in the pre-launch days that also linked to the text of a letter. The letter was from Marco Pollo to none other than Merle Ambrose, concerning a certain golden city...
The bit about rewriting the dialogue with the Aztecosaurs in Xol Akmul seeing visions of Morganthe chaining the Lords of Night in Azteca & Xibalba brining doom to Azteca to come, that's a very good call! I didn't think about that earlier. Eh. Nevertheless, go for it! That really brings the timeline between the story arcs' events in W101 & P101 a bit more in line with each other in the prime Spiral continuity. Plus, I agree that many events taking place in P101 shouldn't contradict those in W101, being that they both take place in the same Spiral we've known & loved.
I also did note about Marleymite in W101, seeing that the batches were made in the Isle of Dogs, I'm presuming a new shipment of Marleymite was placed in Polaris' Walruskberg Harbor before the events with The Rat(Rasputin), yes, Blind Mew?
Well, one of it's side quests I did in W101 made me instantly remember making Marleymite to feed the rebelling Kurgha tigers demanding bad food for their fights in the war against the Armada in P101 as the crates of it were delivered, which helped fed Captain Franklin and his stranded leftenants, Barrow & Crozier, on their journey to discover Polaris, not knowing it was already discovered. Guess he's slightly delusional in the head, even in hunger. Still, the Wizards helping their slightly crazy Captain saved those dogs from hunger & being stranded in a world that's already inhabited.