Magazine info are non canon
It's really not an issue. People don't understand that they're two separate organizations, one dependant upon the other, sure, but each with its own hierarchy.
The WG is a conglomerate of 170 countries, run by the CD families residing in MJ, themselves being judged over by the HKs and ruled by the Gorosei (and IMU).
The Navy is separate from the WG, though founded and funded by it. The Navy as a whole is a tool for policing and control used by the WG worldwide.
The HKs
are the WG's strongest unit. They are a direct part of the WG. The Navy isn't; the Navy is
employed by the WG.
When the POTUS says that his bodyguard is the "best agent" in his administration, he's not counting the FBI, CIA, NSA, nor the Army within that statement; he's only referring to what he directly controls for his safety, which is the Secret Service.
Or, if you want a more in-universe explanation, think of the Grand Fleet.
- The SHs are the CDs. They are the crew, the nakama, the main members. & they call themselves the World Government.
- FMI, Zou, Wano, and whatever other island sports Luffy's flag are the WG affiliated countries.
- The Grand Fleet is the Navy: an assembly of strong individuals following the SHs, and willing to go wherever needed to protect Luffy's reputation or his allies. Which we've already seen happen at the Reverie as well as with Barto and Shanks.
- But if Luffy says that Nami is his smartest nakama, he isn't counting the Grand Fleet. He's only referring to his crewmates.
The Grand Fleet may be an
extension of the Strawhat Pirates, but they aren't
the Strawhat Pirates.
Greenbull is
a Marine working
for the WG. If he were to be made HK by Garling, he would cease to be a Marine and would become a WG-man. He'd be among the strongest HKs, maybe only second to Shamrock. But he'd still be weaker than Akainu, his former Navy boss.
This distinction will soon gain more relevance, as the Navy will have to decide if to fight alongside the WG in the incoming Final War, or if they want to secede in pursuit of their own idea of how the world should look like.