[compman775]

Take a look at definition 1 in your post.

[ars]

Affirm means to say it [again] (without adding any more information). It basically means "Yes I really did/do mean it".

Confirm means to check again.

[burgerbrain]

The way English works, not all of the dictionary definitions for a word need to apply to any particular usage.

[topbanana]

I think all dictionaries work in this way, not just English ones