That is an interesting workflow, @ChrisKeefe, thanks for sharing!
@ilhem (and anyone else following along) - I just want to let you know that contaminant filtering has been discussed at length on the forum: Search results for 'control filter' - QIIME 2 Forum, and there is a lot to review on the subject.
I would recommend reviewing the first page or so of those posts - there are many opinions on this matter, but I think that there is sufficient reason to at least proceed with caution when attempting to filter based on control samples. I think @Nicholas_Bokulich summarized it best here (link):