MIENS-compliant sample IDs aren't guaranteed to work with all tools, so the general problem I described above still stands. See my response above for two examples of this -- both MAFFT and PHYLIP don't work with longer IDs, even if they are MIENS-compliant. The issue is especially apparent with PHYLIP: IDs can only be up to 10 characters in length, so clearly a MIENS-compliant sample ID could still be incompatible with a plugin running PHYLIP. Thus, plugins need to be responsible for re-mapping IDs -- there isn't an ID naming standard that will satisfy the requirements of all bioinformatics tools that are wrapped by QIIME 2.
I'm happy to discuss this more on the dev call!