I think really to get answers you have to break down the alchemist abilities that use things in vials/potions:
1. Extracts. I don't have the APG yet, but what I read in the playtest and on d20pfsrd.com it seems like using an extract is like casting a spell. Most spells have some sort of material component that has to be used, and no game has ever gone into detail about how the caster retrieves those items. It is just generally understood that the person can retrieve them and cast the same round without penalty. They have gone to great lengths to describe extracts like spells. Here are some key texts: "they behave like spells in potion form" "An extract is 'cast' by drinking it"
I would assume this applies to extracts that are already created. If you are trying to create an extract in combat then that is where you will suffer penalties etc.
2. Bombs. These have their own rules about how they can be used. It states clearly that creating and throwing a bomb provokes an attack of opportunity.
3. Potions. Everyone adheres to the same potion rules.
4. Mutagens. I assume these function like potions.