(Sorry for posting on the same thread ina shurt time but I have aquired intresting news concerning the question) In a thread asking pretty much the same question, Blind Mew shed some light on this situation. Here is what he said:

Valencia is a big world - like Skull Island, it has many skyways. The main plot has at least 2 more visits to Valencia planned, each to different skyways where there's a lot more going on.

For Book IV, my main goal was to get you to see Valencia and the Armada up close, and to give you some pretty strong indications of what they intend to do to the whole Spiral if they win. The trick was finding a way for the pirate to go to the home of the big enemies in the game and get out again logically.

Having you go in the front door, fight the Armada full on, and escape strained my disbelief, especially so early in the story: if the Armada is as big and powerful as we say, they'd just crush you. So the entire interlude in Valencia was envisioned as a heist, or the heroes' trip to the Death Star in Star Wars: get in, do what you need to do, and get out before the Armada realizes you're there.

Sure, Phule does find you, but he's not the most... reliable of clockworks.

Don't worry, you'll see a lot more of Valencia. All in good time...

And here's the proof!

At the very end of the storyline, you have to find Meowiarty in order to decode your next piece of the map. However, his cipher leads to the following message...

(Spoiler below, you must use ROT13 to find it out)

V xabj ubj gb qrsrng Xnar. Svaq zr va Inyrapvn!
-Gur Gbl Znxre