We do our best to make sure the scenario listed doesn't happen. For instance, on Windows, after a writer is closed, we apply the Mark-of-the-Web, apply SafeBrowsing checks and finally call a system API which may trigger an anti-virus check.
On the Mac, we apply the equivalent of Mark-of-the-Web. You may have noticed that when you open the file, sometimes it asks you to ensure the provenance of the file?
Basically, it's a similar procedure as for file downloads.
Edit:
I forgot to say that "sensitive" directories are not allowed. Think C:\Windows, etc.
https://source.chromium.org/chromium/chromium/src/+/master:c...