I think this is not directly possible.
Though, a workaround is to use an intermediate surface which is glass, combined with emission (as this setting darkens the surfaces).
Then, bake (transmission) from it to the target plane.
A and B are inverted from initial setting
As (poor) explanation, my hypothesis about why it works is here:
The transparent BSDF shader is given special treatment. When a ray
passes through it, light passes straight on, as if there was no
geometry there. The ray type does not change when passing through a
Note that, while semantically the ray passes through as if no geometry
was hit, rendering performance is affected as each transparency step
requires executing the shader and tracing a ray.
So (maybe), from the raycast point of view (actual or calculated baking cage) the A surface keeps the ray black whilst going through it, except for the rays it diffuses itself.
Is it a bug or unmanaged situation, I don't know.
As opposite, the glass surface receives and keeps actual rays and can transmit them.
Additionnally, we could except that a setting where A is alpha driven mix between glass and diffuse should work (in the initial A on B on C case) but it does not.
Note: edited also because I was wrong thinking changing "film" parameters was needed.