Keep in mind that Center Neptune (and the Crescent Coral Base) can MOVE. So even if Zoltar knew its location at one point, it might be in a different location the next time he went looking for it.
There are only two episodes in the original series where we see them using the rocket engines to move Crescent Coral Reef, and one of those didn't make it into BotP. The second one, though, was made into Invasion of Space Center Part II. They obviously don't succeed in moving fast enough, but they do try.
Anyone who wants to rewrite that episode to make sense has their work cut out for them.
Hmmm. Yes, there are certainly fish swimming past the windows during "Nambu's" briefing to G-Force, and after that scene, we do see the Phoenix departing from Center Neptune. But, is it actually stated that the briefing is taking place at Center Neptune?
I don't think it was.
One could make a claim that it's possible that G-Force met up with "Nambu" at some other non-secret and far less important facility, that just by coincidence happens to have some underwater windows. And after, G-Force then went to Center Neptune themselves (although this was not shown) and departed for Exor in the Phoenix.
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