Question 2: Affection reduces crafting time substantially. Jaesa's bonus only reduces her crafting time by 5%, so if another character is 5000 or something and you just got Jaesa, chances are she will craft slower.
Note, my question wasn't specific to crafting items, but asking about the efficiency bonus in general. Specifically, relating to Jasea's Archaeology (gathering skill) efficiency bonus on missions.
I don't see this being the case. I click through Archaeology on each companion (I have 4+the droid, now) and every single one has the exact same time on each mission. From Pierce with 200 affection, Jasea (bonus to eff) with just over 2k affection, to Vette with only 3k eff.
So, from my perspective, either the bonuses of the individual companions is global for all, or there's a bug somewhere.