as dave points out, when rendering in AE the alpha channel is derived from transparency within the comp. without that transparency, it will render a solid alpha (white).
if you have a matte layer, you can either send that matte to the colorist as Dave mentions, or apply that matte to your comp and render a sequence with the alpha.
there are several ways to apply the matte layer in a comp, in this case i think i’d put the matte layer as the top comp layer, then from the layer blending modes set it to ‘stencil luma’ or ‘silhouette luma’ depending if the matte is white on black, or black on white. then you can render that transparency as an alpha.
if you want to render the alpha as a separate file(s) with a RGB file(s), you can set that up as a second output module when you render… essentially render once, but to 2 separate outputs.
Kevin Camp
Art Director
KCPQ, KZJO & KRCW