After you've submitted it, go to the submission and choose "update submission file". Then, re-upload the file.
It's shitty to have to do this, but that's how you work around the transparency breaking, AND work around resizing. I wish FA would just let you upload the files like that off the bat, but they don't - they have a built in resizer script. So, to get around that script, you have to go back and re-upload it.