bkgrrl00 Most apps (including the system ones) wont appear on the VirusTotal results for many reasons. This isn't a concern, it just mostly tells you how unlikely these files would ever be put through a scanner like this.
GrapheneOS updates on a weekly basis, and with each update you can expect the scanning APIs to detect a different or changed file with each update for some of the apps you have listed. Even if you compare them to the AOSP variants there will be some differences due to some changes GrapheneOS makes to the apps themselves (for example, Settings having its own settings for GrapheneOS features). People are not often putting their GOS system apps into a malware scanner for there to be existing results.
bkgrrl00 then shouldn't the number of "not found" APKs have been much higher?
Not every GrapheneOS system app is different, and in fact many of the system apps are just the AOSP apps which don't get updated often unless there's a security or stability issue. For example, the Calculator or Keyboard probably wont have been changed beyond having a black/white icon, which is why they probably don't show up as never being seen before.