I think many jump to conclusions too fast when they say Ennies Lobby hole was formed the same like the Lulucia hole. Why is there still rocky bridge of the Judicial island remaining above spanning the hole?
Hm I don't know, it's just so similar. What punches a hole into water like that? That stays like that? Kinda nothing does that. But then we saw that weapon made by Vegapunk and used by Wgov.
Like you're saying, it could be a different reason, we don't know. But then we would need a completely new explanation for a thing, a hole in the water, that just stays like that but with a bit land remaining. Wouldn't it be easier to see it as a prototype test, that did not manage to completely destroy all land? Or - as we have devil fruits in One Piece - could the land part be man-made via fruit power?
I think it's just easier to explain the two illogical but same looking things with the same reason behind them, then trying to come up with two different theories.