I don't know how it works for you, but efficiency works that way for me and I have specifically tested it. I don't think affection and efficiency effects time needed to craft, I am completely sure it reduces the time to complete these tasks.
Ok, time to craft, but not gathering missions?
I can provide screen shots, I hit "n", I click on the Archaeology "button" on my first companion, Vette, and all 4 or 5 missions have a certain time for each one. I click on the drop down to select a different companion, and they are all the exact same.
I haven't looked at crafting, because I don't have anyone with a + eff to a crafting skill that I have.
I can provide screen shots if what I'm experiencing is a bug or not.