I was always under the impression this was just a fan theory. Is there anything to really back this up?
The specific lore of the Chaos Emeralds got updated from Sonic2 to 3K. Sonic2 seemed to be planned to explore both said lore and be the de-facto Death Egg arc in general. But production issues came up and the plan ended up split in half, leading to Angel Island's creation. All this is just my assumption from my knowledge of the franchise ^^"
I will say though, there is so much development information available that it's kind of hard to keep track of what's hard fact and what's widespread speculation.
I think the theory of "durr, that green gem is the ME" and "Hidden Palace was a cutscene where you got Super Sonic" got mixed together over the years, where people thought Hidden Palace being important at all, and not just another stage, was a fan theory.
Wasn't there also an interview where they said that they "finally got to use the idea" in Sonic & Knuckles? So if Hidden Palace made it into Sonic 2 instead... I wonder what the franchise would be like now if good old Hidden Palace made it into Sonic 2 and consequently dropped from S&K. Would we have even gotten S&K? O.O
I'm more curious about how they would have handled Super Sonic post-Sonic 2. Going by Naka's words, the original lore would have established that you need to visit Hidden Palace to gain the form. Would later games would have included Hidden Palace as well (albeit with new graphics, layouts, etc.) to allow the player to turn into Super Sonic? Or would they have given you access to the form right away, acting under the assumption that Sonic kept the ability to transform after Sonic 2? And what about other characters going Super, like Knuckles or Shadow?