The assumption you make is that pages that are not indexed have no bearing on pages that are indexed. I am doubtful this assumption is correct. The pages are not indexed due to the noindex tag, but Google clearly crawls and evaluates these and now flags up problems with attachment pages.
This makes sense because Google wants to rank quality pages and good sites. Even if a page is not indexed, it still matters to the usability of related pages.
I think that you are correct when it comes to singular pages which are not indexed. However, when you have a mass of problematic pages with clear duplicate content, thin content and links to itself it is likely to differ. If those problematic pages are hotlinked from article pages, then it seems very logical that this can negatively affect the ranking of the articles. In fact, I used to apply exactly the opposite method to give pages a high/top ranking by stuffing them with links to loads of relevant content. (and which is exactly what should make a wiki so good for SEO)
Basically these are dead end pages. Lets say an article has 20 attachments. So the article has 20 links to dead end pages. While the dead end pages are not indexed, there is an issue: if a user clicks on such link, then they no longer have a path back to the article. They can only see the attachment, click on links to the same page (circular links) or click on history links without content.
We can hide this by disabling viewing permission for guests (which I did), but now we have malfunctioning thumbnails. Which also affects the article ranking negatively. It seems to me that the best would be to have a permission for thumbs in articles, so that we can hide attachment pages without malfunctioning thumbnails.