I never completed the Malistaire Arc in W101, but unless I'm mistaken, these two things don't contradict eachother. The events of Pirate are chronologially after the events of wizard: Thus our interactions with meowiarty occur whilst he is imprisoned, Mooshu's emperor is in a deep sleep, and the aztecasaurs have fled their home. Unless the defeat of Malistaire actually woke the Emperor (which it very well may have, like I said I never got that far into W101) then there isn't actually any inconsistency going on.

MistyDragon13 on Jun 9, 2016 wrote:

This has been debated several times but if you go back and look at the dialogue in the beginning of Xol Akmul, Itzam Halach specifically says that the Aztecosaurs of Xol Akmul fled Azteca to avoid "the Cataclysm to come". This in itself proves that they left Azteca before Morganthe dropped Xibalba. Morganthe was in the shadows long before we realized her as a threat in Celestia; it stands to reason that she enslaved the Lords of Night quite a while before realizing she needed more than just that control to rewrite the Spiral as she wished.

As for the MooShu bit, it's been confirmed that we experience Marleybone and MooShu in the opposite order that wizards do; while we're in MooShu, the wizard is in Marleybone, and while we're dealing with the troubles in Marleybone, the wizard is exploring MooShu. The emperor's cursed sleep is consistent with both storylines due to this.

Bingo. It didn't come out as clearly as I had hoped, but I made sure Morganthe was a problem in Azteca long before the Xibalba endgame. The timelines for the two games are "roughly concurrent," and the example of MooShu and Marleybone is exactly how we planned it.

Pirate101 happens way after Wizard101, so we could say the very end of the second arc is when the pirate's adventures begin.

Proofs:
- Zafaria's Boxe, we go to skull island.
- Penguinia is still in mention with Polaris in third arc, so napolenguin is breaking out at that time.
- When pirates go to mooshu, they mention that it was new that samoorais became musketeers and using guns.
- While wizards do not see any guns in mooshu.
- Azteca\Celestia\Skull-Island, wizards will go to azteca and see monquistadors around the swamps, and lost, monquistadors arrived at the time of azteca, and then they started doing exploitation as we see in pirate101.

also worth showing this map i made, not nice but core elements are shown:

(Sorry, posting images isn't allowed on these message boards per the rules ~One-Eyed Jack)

Moon Lord Robert on Jun 14, 2016 wrote:

Pirate101 happens way after Wizard101, so we could say the very end of the second arc is when the pirate's adventures begin.

Proofs:
- Zafaria's Boxe, we go to skull island.
- Penguinia is still in mention with Polaris in third arc, so napolenguin is breaking out at that time.
- When pirates go to mooshu, they mention that it was new that samoorais became musketeers and using guns.
- While wizards do not see any guns in mooshu.
- Azteca\Celestia\Skull-Island, wizards will go to azteca and see monquistadors around the swamps, and lost, monquistadors arrived at the time of azteca, and then they started doing exploitation as we see in pirate101.

also worth showing this map i made, not nice but core elements are shown:

(Sorry, posting images isn't allowed on these message boards per the rules ~One-Eyed Jack)

There been several theories, including the theory mentioned by a friend of mine that the events of Pirate101 happen years LATER after the events of all three story arcs in Wizard101. It was also mentioned by my friend that they meant to set up the penguin revolution as being the event leading to the Polarian War. Of course, the people of KI made a mistake by making the wizards and pirates being in the same world exploring different parts that they have access to. Let me correct some of the events you mentioned right here:

- Zafaria's box actually takes us back in time prior of the story in pirate101 has begun. Your forgetting that the box is a time traveling device.
- When we visit Polaris as a wizard, Inside a tavern you see Boochbeard's sidekick (forgot his name) sitting at a table waiting for his friend to come out of the bathroom (Hence the hat and sword left on his seat). We can only conclude that by then that crazy ex-emperor is hiding in the mist waiting for his grand return with the penguin revolution.
- In Mooshu, it's possible that by then the new artillery General Tso got from the Armada have yet been widely distributed across Mooshu, therefore it haven't made it inland enough for the wizards to even notice. You're also forgetting that when they originally released Mooshu they mention in their press announcement that this was during the wizard's attempt to cure the emperor. So it's possible that by the time we leave Mooshu, the wizards are leaving Mooshu too.
- In Azteca with the Monquistians, that sailor might have been reported lost at sea when he went out in search for the fountain of youth. If the Monquistians have just started exploring when Pirate101 started, than by story arc two of wizard101 their roots might have spread all the way to Azteca.

We can't fully say how big of a difference in timelines all this happen, but we can say we should find an explanation for the next world where we are in this timeline.