Hi @ja.morillo ,
As a disclaimer, I'm more of a 
person, but there's hopefully some at least methodological insight to offer based off of complex ecosystems :).
You can't pass the method directly into core-metrics (and core-metrics-phylogenetic); these are workflow pipelines. You can run the commands inside the pipeline (I'll be honest and say this is what I do most of the time because I like more control.) Check out qiime diversity alpha / qiime diversity alpha-phylogenetic and the corresponding beta and beta-phylogenetic commands.
I (personally) stay away from DeSeq2. Partially because I'm not an R user. Partially because I dont like the assumption they use to break compositionality for most studies (a normalized number of copies per enviroment.) You could look into a recent discussion around models with random effects and interaction terms:
It does require work outside of QIIME, but it might be an option. It can also be hard to interpret. (But so can ANCOM and any one of a number of other techniques)
Best,
Justine