I thought I could use productivity modules in following recipes but I could not.

Coal -> Carbon Black
Carbon Black -> Graphite

Are these by design? The latter one is understandable as it is described as unfavorable ratio

Both are by design, yes.

Coal --> Carbon Black is intended to be a supplementary way of creating carbon black (as the primary is through cracking or oil processing).
And indeed, the second one is intentionally unfavorable and primarily present to prevent deadlocking if you have no way of voiding items.

Thank you for clear explanation!