The main reason Clinton supporters (Media) and Trump supporters disagree on this, I feel, is just a difference of what they're expecting and exposed to. Most supporters on both sides are reasonable people, but both suffer from cognitive dissonance. We know intuitively it is virtually impossible to deport literally everyone, and the amount of resources this would cost is insane, especially when half the public disagrees with it. So when Trump tells us he wants to deport literally everyone, we already correct this in our mind. We know him and The Art of the Deal well enough:
"Ah there's Trump again starting with the hyperbole. He'll move to a less extreme stance later in the election"
Clinton supporters, on the other hand, don't have this background information and are biased to be anti-Trump. When they hear Trump say something like this, they take him completely seriously. So now Trump is actually pivoting to a less extreme stance, all Trump supporters feel like "Yeah, this is what I thought all along", while the Clinton supporters feel this is a large change.
I think the second problem here is the negative connotation of "flip-flop". He did indeed change what he said, but if so many supporters accurately predicted a pivot before it happened, it's clear that it doesn't come out of the blue.
In the end, it's just another symptom of the mainstream media taking what Trump says at face value, and arguing about those main points without the nuance of placing it in the right context.