I believe they do account wide (owner wide) assessments. So, Yes, I believe it matters. Certainly seen an across the board (all sites) hit this week. The only way this can be explained is an owner wide process.
It's dumb. But then it's about Google being overly concerned with keeping spam stuff out, rather than being concerned with ensuring good stuff is prominent. (You have to think about this carefully, because the meaning is subtle).
We have sites on different, but related topics, to make it easier for our visitors to find what they need, and no more if they wish, or to look at the related topics, if they choose.
Guess what? The sites are interlinked somewhat.
It's the only way to present the related content without duplicating it on various niche sites. So, my bet is we keep getting hit.