As mentioned in the comments, I realized that Premiere Pro was the wrong tool for the job. Thanks to Florian I got started with ffmpeg.
For the sake of any future users who might want something like this, I thought I'd share my solution.
The following Command helps me convert my wmv source file to mp4 with a png watermark in the bottom right corner and the source video negated (colour inverted).
ffmpeg -i source.wmv -i logo.png -c:v libx264 -crf 23 -c:a aac -strict -2 -q:a 100 -max_muxing_queue_size 9999 -filter_complex "format=yuva444p,colorchannelmixer=aa=0.8[logo];fps=fps=30, negate=1[flip];[flip][logo]overlay=x=(main_w-overlay_w):y=(main_h-overlay_h)" output_file.mp4
I also made a gist with the broken down commands for each of my requirements. ffmpeg is blazing fast too!