It appears that as of Safari 15.2 (or 15.3) and/or macOS 12.2.1, this issue (along with several other Storage issues) is resolved. Here is an example demonstrating that "local" and "sync" have different contents (I've omitted the code that got it that way because it should be obvious).

I have a related issue. I'm automating a third-party website that generates reports. The reports are downloaded to the user's computer as ZIP files. I want to grab the zip files and send them on to my server for processing. How can I accomplish this without using the Downloads API?