Hello @jwdebelius ,
Wow, that's a ton of useful information. Thanks!
Indeed. I also saw that point in Lin and Pedadda's ANCOM-BC paper, as well as in this fungal metataxonomics review. I also found this review very useful.
So the problem is that the field moves so fast that, even in peer review, there is not enough capacity to keep up. Thus the responsability to do a good analysis regardless of what we see published is ours (I think this can really be applied to science in general).
Thank you for sharing your thoughts. Knowing that publication lag is particularly present in this field, I can confidently act accordingly and discard in my literature review papers that in my judgment are not analyzing the data as I believe they should be. 
It is wild how much I am learning in this forum. I hope it will help my future analyses/articles to be scientifically rigorous.
Cheers!
Sergio
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Side note: your footnote 1 reminded me that I recently came across this paper, and it is being very useful for me to understand how some methodological concepts are applied 