I only do still images.. And haven't as yet tried anything like that in recent time's.. Use gimp and photofiltre for most of my postwork but Gimp layer's pretty well so shouldn't be an issue. Though I'm new enough that I'm not certain what you mean exactly by an alpha channel. It used to be I would just set my background color to a color I could easily set as transparent. But that has it's own issues. Loss of color quality etc..

Mark.