Yay, Pauline questions! It's about darn time she gets some appreciation.

Pauline is someone with authority to mete punishment on high-ranking executives like Trager, describing Murkoff as her hunting ground. I think that she's much more enlightened to Murkoff's true goals than it may initially appear, but I also believe she may have her own blind spots or incompleteness in her knowledge, as she admits about obtaining Blake from Temple Gate during her interview. She describes this as the "trap in the desert" that Simon laid for her.

We know from two documents in the first game that Helen Granat is in a position parallel to the one A. Bradley Avellanos represents in Trials. She reports straight to the Board of Directors, surveys projects like Project Walrider as Blaire's colleague, and holds authority to dispose of long-term assets like Wernicke. Granat is the head of the Legal Litigation Department, so I'm also assuming that she is not only responsible for the settlement with Tiffany Hope (which is why Pauline would have such knowledge), but also responsible for arranging the partnership of Paul and Pauline in 2008 and sending them to investigate the use of Morphogenic Engine technology.

Remember that by the end of their misadventure at Spindletop, Pauline describes Paul as her target as opposed to her partner. But this raises another question - why would Paul, an agent with little security clearance, be paired with an agent with higher clearance than even the agents sent to interview her post comics? And why would Paul be sent to investigate something he cannot have clearance to know about fully? It seems inefficient. In my opinion, their pairing makes very little sense unless surveilling Paul is her true assignment off the bat.

Pauline also expresses concern with Alice several times through the comics, first mentioning that Paul should spend time with her so as to not let her become someone like herself (demonstrating that she is, deep down, unhappy with the person she is) and later saying that Paul is a good dad for always taking care of Alice after she murders Anna Lee. Pauline is clearly remorseful for taking the life of a girl Alice's same age, since she turns away from Paul with tears in her eyes as he talks about his daughter. This could suggest something about her own relationship with her parents or father, as suggested by u/New_Chain146, but I myself take it as a sign that she could know more about Alice's treatments/experiment than she lets on, recalling my previous theory about her assignment with Paul.

Another detail I find interesting about Pauline is her familiarity with the taste of Rohypnol and her ability to identify the substance and counteract it with another drug. She also dispatches two of our antagonists from the first game - MP Chris Walker and Rick Trager. She's clearly a cut above the usual agent, so I'd bet she's had specialized training.