Thanks for the response guys.
I’ve tried all the suggestions, and still, no alpha. The reason for wanting to use compressor is its ideal for multi-sequence, multi-codec large batch exports on large projects (which thankfully isn’t the case here). I’m using Chroma Key filter in Final Cut, and do not have or use After Effects. It does work when I export using “Quicktime Conversion” with identical settings, so I’m led to believe this may be a bug with compressor. Oh well, thanks anyway.