If I can jump in @colinbrislawn, the good news from the answer you linked is that I got joint filtering in QIIME 2!
In terms of p-min-frequncy; I tie my minimum sample frequency to my rarefaction depth (if Im rarefying to 1000 seqs/sample, I want sampels with at least 1000 sequences). Some one will absloutely be mad about your rarefaction threshhold (mine is reviewer 3 as well!).
In terms of feature discards, it depends. I tend to filter my features more heavily on other criteria. For example, features I cant classify to at least phylum level, reads that don’t insert into a phylogenetic tree, or reads that are assigned to chloroplasts or mitochondria. I might also filter super rare features (singletons). This is the table I then take into subsequent steps.
So, I’d rarefy it as a normalization approach for classic diveristy metrics. I’d filter it again a little more aggressively for differential abundance/prevelance, aitchison distance, or DEICODE.
Not sure if that helps or makes this more confusing.