Watching the scene again, the upgrade seems fine. Yes, it's a singular scene across most of the continuity. No, that's not grounds for dismissing what's being said there.
When the Naljian talks about how humans can only perceive "only" 3 dimensions, she's pretty clearly talking about spatial dimensions like up-down, left-right, and forwards-backward. When Ben asks for clarification on how many dimensions there are, he's still referencing what she just said, so they're still talking about dimensions of the same nature. I'm not sure what this "we're not sure what they mean" rhetoric is about. There are more than 3 spatial dimensions (the ones humans can perceive) and at least 26 based on piecing together the conversation's basic sequence. Given that these are specific directions they're talking about, the Omniversal Force extending endlessly throughout every direction would apply as well.
I'm not sure who or what would scale but the the cosmology being Hyperversal seems good to me.