Here is my opinion on the matter.
Let's use a similar event with different objects. Take 2 full size, identically built cars. Park one car. Speed the other car up to ... let's say 60 mph. Ram it into the parked car.
Which car is going to receive the most damage? The parked car, of course. Is it because the moving car is harder than the parked car? No. We set the whole thing up, using identically built cars. That means they are of the same hardness. So, why would the parked car take on more damage in most cases? Does anyone know the mathematical value of force, when applied to a stationary object? If so, now would be a good time to share it. (I might not have said that correctly, but I'm sure someone has a clue what I am asking for.)
Now. Who hits the ball softly to break the rack? Nobody I know. They use force to shove the cue into the cue ball and cause it to move forward at a high rate of speed, using it's momentum to move the many balls at the other end of the table.
Also, many things actually become harder on impact. So, a softer object can actually be harder on impact. Consider the hardness of an airbag being placed against your skin with air in it, versus an airbag being exploded into your face. Which is going to be harder? Does the force of impact make a difference in the hardness? You bet it does!
I totally believe it is miscues and/or momentum power coupled with tip size that cause these indentions, in most cases.
Years ago, long before I ever heard of phenolic, a pool hall we played in had regular mudballs, as always. After a certain amount of use, they had to be replaced, due to chips and dings, dents and flat spots which made the ball practically unusable. This was in the early 1980's. I remember a day-long discussion over the shape of the 1 ball, which most folks tend to put at the front of a rack. It had flat spots on it, which caused it to roll funny. The owner of the small restaurant/pool hall said he had to buy more 1 balls than any other numbered ball. Why? The impact of the cue ball caused flat spots on the 1 ball, after so many direct hits.
A cue tip is smaller than the ball and therefore, instead of just flattening part of the ball, when it gets to the edge... ESPECIALLY if the hit is a miscue, the edge of the tip could possibly indent the cue ball, I would think.
As for what is harder... phenolic or a cue ball... You need to add momentum and smaller size to your equation.
If you don't like what the phenolic tip is doing to your cue ball, the fix is quite simple. Don't allow phenolic tips to be used on it. A cue ball is not cheap, but there is no reason to make a year-long issue of it. Just buy another cue ball and get rid of the phenolic tips.