At the end of last year, redpaw made a post about the alpha channel not working in a prores4444 file.
https://www.vegascreativesoftware.info/us/forum/alpha-channel-not-working--113478/#ca701374
I had to re-visit an old project that has a 2sec shot transition and am having the same issue. I have V16 build 361.
https://www.dropbox.com/s/4sbciwda9oq8u6d/Shot3-Transition.mov?dl=0