I believe your problem is because you are switching the blending mode to Screen. Screen requires something to screen, and if you delete the video underneath the Screened clip, there is nothing for it to screen and it becomes opaque again. You can see this if you switch the Program Monitor to display over a transparency grid instead of black (click on the wrench int Program Monitor and select Transparency Grid).
Rather than using Screen, set the blending mode back to normal and make a mask in the shape of the white bar.
Did you try Animation with Millions+ ?
I am surprised that a PNG Sequence did not work for you!
How have you made a Sequence that contains alpha transparency?
What are you going to use this export and alpha for?
Will something you can create in Titler work for you?
I have never needed to export Alpha from PPRO because I use After Effects for that ....so I dont really have a tried and tested solution for you ( sorry) and I am not in front of my NLE at the moment
I think I agree with your Screen Blend assessment of the issue.
You are right!! I come from FCP7 where if something is in screen mode, black is treated as opaque whether there's anything behind it or not. So when I export it with an alpha channel it's transparent. But as always, Adobe is doing things differently.
What else does Adobe "as always" do differently?
I know Adobe Photoshop is very different to FCP Photoshop
FCP7 is very different to PPRO also . eg. PPRO is loved and supported by ADOBE ....and FCP 7 is an abandoned orphan courtesy of Apple
Just winding you up IvanThe ConvertEditor.