That is an interesting point, today we do flag every validation warning for 404 pages. In the next release we will not flag things like Duplicates, or canonical issues, however we still flag other violations, mostly because we still want to make sure that those files are "user friendly" so we want to check for broken links, have a decent title, invalid markup and other related things.
I guess one interesting thing is that you can achieve that today and filter any status codes you care or not care about. For this:
1) In the violations summary report, use the "Actions->Open Query" option to open a new tab with a "customizable" query builder
2) In that tab you can add a filter "Status code" "Equals" "OK" that will basically show exactly what you are looking for. (or you could say "Status code" "Not Equals" "NotFound" which would only remove the 404's).