There are few things that are more controversial in evangelical circles than common ancestry of humans and animals. There are few things that are less controversial everywhere else.
Of course DNA comparisons are empirical! They are carried out by observation, experiment and measurement. To claim that DNA comparisons are not empirical is to claim that geneticists do not do what they say that they do, in other words, it is to accuse them of lying. If you’re going to do that, you need to provide credible evidence to that effect, otherwise you’re just promoting conspiracy theories.
As for them being a “nonfact,” can you come up with a credible explanation other than common ancestry as to how the human genome and the chimp genome could contain two hundred thousand endogenous retroviruses in exactly the same places?
In any case, even if the evidence really were ambiguous on this matter, it is still something that is investigated by observation, experiment and measurement. This being the case, whether it is true or not, it is still a mechanical aspect of evolution and not a philosophical one.