They aren't saying "we see these things now, so they must be good" but rather things like "we see these selected for from 9kya to 3kya, but from then to the present they were selected against"; they are specifically looking at how apparent selective pressures changed over time.
> the idea that things that "were selected for" in the past can be determined by evidence
When the evidence is a copious selection of ancient genomes, distributed over both space and time, they certainly can be.
