Phylogeny is different than similarity. There are poor/incorrect methods of inferring phylogeny that use similarity. But the best methods use nested clades instead, and this is usually what we mean when we talk about phylogeny. It turns out that these two methods actually produces different trees.
So this turns out to be 100% false.
First, these studies do not assume evolution. Rather, like all modeling efforts, they make quantitative predictions with the evolutionary model. We then compare this to other approaches like similarity. The results of this comparison is what tells us which model works better. There is no assumption that evolution is correct here. Rather, we use the data to determine if the theory of evolution helps us understand evolution. It is a direct test of your theory that phylogeny is equivalent to similarity. We find your hypothesis is FALSE.
Second, it is 100% false that the input to phylogeny is just similarity and the assumption of evolution. Phylogeny algorithms require the full sequences, because the need to determine how nested clades cluster sequences. Nested clades cannot be inferred from similarity. I understand that this is all new to you, but your understanding of this is incorrect. You are wrong.
Remember, no assumption is made. The data tells us which model works better. Because similarity and nested clades produce different trees, we can then ask which type of tree gives a better description of our world. Here are three articles that carefully do this comparison, and all come to the same conclusion. Phylogeny (by nested clades) is about two times better at explaining the function of proteins than similarity.
Do not fear the evidence @NonlinOrg. God is the author of all truth, including this.