Been doing this for years... from After effects CC
Composition, Save frame as, File, Photoshop, RGB+Alpha etc - and its worked fine exported with transparency like you'd expect.
Updated Photoshop CC this morning and suddenly alpha channel not being recognised...
Bug...or have I gone mad in the last 24 hours??
Maybe I misunderstand your question but Photoshop CC opens psd files with Alpha Channels just fine here, so it seems likely that the issue is with the files.
But you seem to be mixing Alpha Channels and Transparency – so what are you talking about exactly?
Could you post screenshots to illustrate what you are doing and what results you get?