Thanks for your response Rick. Media Encoder would be nice to use for sure, but the same problem exists in there. The mediafiles have a different width, but the same height. To scale them, the width has to change the same percentage as the height. Just like the examples in my first post. You can't set a scale percentage in the Media Encoder presets as far as I know. Just like an output module in AE, you can only scale to the given size in pixels. As the source files have a different width, this won't work.
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