That's how it was conceived, yes. That's the official story. I don't think that's the whole story.
"I'm Only Sleeping" was conceived as a song about drugs. The final song, however, is clearly about sleeping in in the morning. How a work of art was conceived and how it finally ended up are often very different. Why does everyone trust what the Beatles and their associates say so much? They've been known to lie, so why always assume they're telling the truth at all, let alone the whole truth?
I've never subscribed to the belief that the artist's original intentions are the most important thing in determining the meaning of a work of art. I don't think intentions matter at all. What matters to me is the actual content of the final work. If it's not in the work, it doesn't count. That's why I like making fun of Pete Townshend's compositional skills, even though I respect him musically. He changes his mind after he finishes a work and tries to convince people the info was there all along.
I think "Come Together" is about a kinky stoned threesome, and that's what I'm sticking with.