I feel like I should know the answer to this, but obviously I don't. Hence, my question.

How do preferences come into play with respect to APs? Are they a modifier of the value of APs? In other words, would 10 APs have more value on a recruit who you are "very good" on a handful of preferences than they would on a recruit who you are "very bad" on a handful of preferences?

Or do preferences come into play with signability? In other words, a recruit is "very high" on both team A and team B, but is very good on a handful of preferences with A, but very bad on a handful of preferences on B?

Preferences are just modifiers on your recruiting actions (AP, HV, CV, etc). So if 2 teams are very high, then the preferences are already accounted for in the results.