What version of PR are you running? The transparent video should not be an issue. It is getting 2 tracks to show at the same time.
See "Show Multiple Caption Tracks" this thread:
https://community.adobe.com/t5/premiere-pro-discussions/faq-workaround-nesting-to-apply-effect-controls-to-caption-track/td-p/11935335
Basically, in Sequence 1, transcribe one speaker and create captions. Set the font color to what you want. Disable the video and audio. Nest this in Sequence 2, where you transcribe the other speaker. Caption and color. The first speaker shows because it is nested. The second is the captions in the second sequence.
You can also adjust position differently if you want.
Stan