I sort of disagree with this but it is just a matter of differing perspectives, I suppose. One advantage of "doing it all in QIIME 2" is to store it all in provenance (and these could be changes that you could consider contributing to the q2-dada2 source code, though doing so would require 1) approval of the q2-dada2 developers and 2) a little more work to expose these options so get in touch if you want to contribute).
Here is a topic where I described the process for a similar problem, and link at the end to the file that should be altered in your local branch:
Or here is a tutorial for importing dada2 objects into QIIME 2:
