It seems like the issue has been resolved in recent WebKit commit. https://commits.webkit.org/283383@main Hope it gets included in the public release soon.

Here is demo project that saves files into extension. https://www.dropbox.com/scl/fi/8q42b853zjp6wcufhxatm/file-uploader-main.zip?rlkey=j323aip9szuljs5drb3hrrhed&st=o2dparl5&dl=0