It looks like the source of my confusion was the assumption that the addition of the header "X-Virus-Scanned: Debian amavis at tait.net.nz" to the message meant that the message had been virus-scanned
If your ClamAV instance runs with "ScanMail true", and your Amavis instance's @keep_decoded_original_maps include MAIL-UNDECIPHERABLE (which they do in upstream as well as on Debian), then the message had been virus-scanned. But Amavis does more than virus-scanning. For example, one might have @banned_filename_maps that do not indicate viruses per se. If Amavis detected (potentially) ambiguous content, it means that it might see different filenames than the receiving MUA, so the message is considered unchecked as a whole.
