Having run a few scenarios with different Venture Captains assigning missions, I've noticed several of them come off as being jerks/elitists/aloof/etc., while the Faction heads tend to me more supportive.
Dreng, wakes them up at odd hours
Aram Zey, total jerk
Kreighton Shaine, airhead
Is this intentional? More motivation to be in a faction? Do Pathfinders join factions for validation or warm fuzzies?
For the record, Kreighton Shaine is a lunatic, not an airhead. :)
The overarching theme of the Pathfinder Society is "Prove yourself," and the higher-ups seem to have very little value on the low-ranking members of the society. (Hence: Shadow War.)
The factions themselves might value their agents a little more, but that's mostly about their personalities, I believe. Note that not all the faction heads are members of the Society. For example, Guaril Karela is a "friend" of the society rather than a member, and often the Szcarni and Pathfinders have enough in common to work together.
In essence, I think this is like real life. Your character has their own interests outside of work. Now, if you can use your work to advance those interests (like, say, one might if they worked at a print shop and spent a lot of time printing out massive vinyl posters to support their local PFS play - which I do not do, incidentally), why not?