As far as I can tell, the article is extremely misleading, for two reasons:
1) The article imagines that Loschbour (WHG) and Stuttgart (ENF) completely represent the modern European gene pool. They pretend that no steppic introgression ever occurred, so of course they do not even consider attributing any DNA shift to it.
2) The article claims that an allele originated in a particular group if its background occurs in that group, even if the allele itself never did. The article does not consider the possibility that the same background may have been present elsewhere (e.g., the steppe) as well.
This is what the articles says about pigmentation -
This is what the article says about LP -The derived allele upstream of OCA2 (rs12913832 in HERC2) is associated with blue iris colour in Europeans42 and light skin pigmentation43; both this variant and its linked variation show that Loschbour carried the predominant European haplotype (Fig. 6a). The derived allele in SLC45A2 non-synonymous rs16891982 is associated with lighter skin pigmentation and increased melanoma risk in Europeans44, 45. No ancestral genome carries rs16891982’s derived allele, but Loschbour carries the haplotype that, in present-day populations, is linked to the derived allele (Fig. 6b). Therefore hunter-gatherer populations likely contributed both OCA2 and SLC45A2 advantageous alleles to the European gene pool. This agrees well with these populations inhabiting northern European areas before the arrival of southern farmer groups. Lighter skin pigmentation has been proposed to be advantageous in northern latitudes to sustain vitamin D3 production in low-ultraviolet environments46
So what they are saying is that a group of alleles can be used to deduce if one of those traits likely appeared in a certain group or not. Since they mention LP in an individual of steppe ancestry we know they did take steppic introgression into consideration.It is known that the two derived alleles associated with LP in Europe (in rs4988235 and rs182549)53 are absent in the two ancient genomes33 and are not observed in Europe until ~2300 BC in an individual of inferred steppe ancestry17. But the European tail includes a large number of alleles in the lactase enhancer region and the LP haplotype (chr2:135859371-136740900) that are exclusively present in Stuttgart (65% of Stuttgart specific targets; Fig. 6c). Thus the haplotype that is today associated with LP in Europe originated most likely in this genetic background, which we detect only in the Stuttgart farmer, although this individual itself did not carry the LP allele.