I quite like this plugin, and have also run into this issue. For now, I have coded a PowerShell script I can call like a function, using Write-S3Object (Which auto-detects file size and uses multi-part upload as necessary) to upload a file or folder. If this is useful to others I'm happy to post it here.
Documentation is in the file. Note that you'll probably want to find a different way of handling credentials than what that file implements, or at least switch to using PowerShell Secure Strings