I've thought about this more, and I had a similar-ish idea.
Instead of showing all of Mr. Manager in one go, how about partial reveals?
Like, it's all black, and *someone* is talking to you, but you can't see who.
Then maybe some eyes in the dark are visible.
After a little while, you swear you saw one eye change colour.
Then the light are on (but he's not swapping assets yet), so he looks offputting, but maybe he's got injuries in the backstory?
Then, finally, all the moving bits and assets swaps are going for the last part of the dialogue, adding the climax to the transformation.
You'd need to have the dialouge and background music match the tension level of the visuals; but that would be my suggestion for making Mr. Manager more impactful at the start of the game.
At the moment I find him less scary, and more just gross and confusing; but I think that's because of the missing tension I've just tried to explain.
A reference interaction for the sort of feeling I'm describing would be the opening conversation with Flowey in UnderTale; but with more layers.