I have worked at a sequencing center before. DNA contamination is easier to mitigate because the lab disposables aren't made out of what you are testing. Disposables are almost always plastic and tend to have minimal DNA contamination. Environmental DNA contamination is largely mitigated with PCR hoods and careful protocols/practices. However, these procedures don't mitigate DNA contamination at the collection level, which is likely where the statistical models you mentioned help.

I can't imagine wafting your hands over the tubes would change the plastic amounts substantially compared to whatever negative controls the papers used. But again, I am not an expert on this kind of analytical chemistry. I always worry more about batch effects. But it does seem like microplastics are becoming the new microbiome.