Hi @Alfred.Burian,
Thanks for bringing this up!
Without wading too far into this debate, I will point out that rarefying is not always inadmissible, particularly for unweighted UniFrac and other beta diversity methods based on presence/absence of features. This is actually also shown in Fig 4 of the article that you posted, though for other distance methods other normalization strategies perform better.
Second, what you describe is the qiime diversity core-metrics-phylogenetic method, which requires rarefying because it also computes alpha diversity metrics (which must be computed on rarefied data). It is possible to circumvent this behavior by running qiime diversity beta directly on a non-rarefied table.
I have raised this issue to support other normalization strategies for beta diversity, and this issue to add some description of this to the tutorials.