Uh-hun..... and what AE and OS versions are you currently running, right down to the last decimal point?
And since media players are typically incapable of displaying alpha channel information, it would be interesting to know how you determined it was there.
After Effects 22.214.171.124
OS X 10.11.1
If I open in Quicktime/VLC, it shows a black background and as expected. If I select the file in finder and press the space bar, or click the quick look button, I see the alpha channel. Finder's quick look shows the alpha channel on most files that support alpha and/or transparency.
I just did a test with a video exported from AE set as RGB+Alpha ProRes 4444 and the alpha channel was interpreted correctly upon import back into AE. So, it must be some export setting in FCP. But of course, I didn't export the video. I don't even have FCP on my machine.
This is an example of Finder's Quick Look function correctly showing an alpha channel. You can see my beautiful desktop image with some OS X gaussian blur shining through. This is not the content I'm working with, since I can't post that here. However, the video in question does display with an alpha channel when viewed this way.
I have the same problem in Adobe CC 2018
Export from Final Cut Pro 10.4 as ProRes 4444, test in finder with space to play video, alpha is definitely there and transparent. Bring into Adobe Premiere on PC and it's black. Interpret Footage in PP and alpha options are greyed out so it is assuming there is no alpha.
Driving me mad.