This theory will discuss the recent events about Vegapunk’s design, his connection to the moon, and how this could point to Vegapunk being the creator/captain of the Space Pirates.
To begin, we are introduced to Vegapunk as part of the elongated head tribe (as far as we can assume, considering his head size, and how it constantly increases as noted by Dragon in the chapter, both traits of the elongated head tribe). Moreover, we know that in the Enel cover story, there are Space Pirates who have the elongated head tribe symbol.
Now, those Space Pirates are shown to be animals of sorts, specifically, Cybernetically Enhanced animals.
We know that Vegapunk, when he was young, made cyborg animals in his homeland of Baltimore, and not only that, but Vegapunk has a lot of symbolism to the moon, seeing the different versions of Vegapunk and their connection to the moons, his connection to Ohara and their connection to the moon (the globe), and overall the robots created by a scientist from the homeland of Vegapunk that went to the moon as well (same ones as in the Enel cover story).
With all this in mind (his cybernetic animal creations, his connections to the moon, and the Space Pirates jolly roger), what if the Space Pirates that Enel encounters, are actually creations by Vegapunk and he made the Space Pirates, with the symbol and all, to explore the space? The Space Pirates could actually have been made by Vegapunk.
Therefore, Vegapunk might be the captain of the Space Pirates!
*Theory by Kikoco