Recommendable production codecs for Adobe video products
Ut Video is an editor friendly lossless video codec and is a good choice for in house production as an intermediary. It is fast, open source, actively developed, supports RGB(A)/ULRA (for your alpha channel requirement) and YUV colorspaces, and is available for Windows, OS X, and Linux. You can install it on Windows and it will show up in Adobe Media Encoder, After Effects, etc. I don't know if it will fit all of your needs, but it is worth a try.