Hi Mr. Jordfald.
What Frank said:
Aperture will preserve the alpha channel in an image but will not create one or work with it within Aperture.
does not indicate that you cannot use Originals that have an alpha channel in Aperture. Afaik -- and you should test this yourself -- if you assign an Image with an Alpha channel to a book, and print the book, the Alpha channel will be used in the printed book.
That isn't the workflow we would all like, but the compromise should work (again, afaik -- please confirm). Whether it is worth it for you, only you can decide.