I can't agree. James was onscreen with the boss for about 30 seconds. The fact that the boss didn't acknowledge him could just as easily be an indication that she's a grumpy, unpleasant person who doesn't like Bella... which is exactly what her 'Holier-Than-Thou-Hilda' nickname suggests! Likewise the man sitting outside the library looks at them because they're having a loud argument right next to him. This isn't inexplicable behavior, it's normal behavior you're reading too much into.
In the end, there's no actual evidence James was a delusion; it's just a guess that can't be disproven at the moment. If Bella had exhibited any signs of that sort of madness in the present day, I'd be more willing to entertain it. But we've seen a lot of contemporary Bella, and she's always been lucid and sane (if obviously troubled). So unless we assume her mental problems were successfully treated between the flashback and the start of the game, there's no reason to doubt James was real in the flashback.
I agree Burke would be foolish to try pressuring Maya, but there's reason to believe Burke isn't all that bright. I think
mindern has the right overall idea, it's just a question of how best to position the players so the plot will progress on schedule. As I see it, this is going to be a long arc. Season 3 will be about building up tension while Season 4 will be about actually addressing the fundamental problems once and for all.
Given that, it seems like the simplest option will be for Burke to offer to help Maya but say it will take time to set up. This will lead to Maya working as an intern in some companies friendly with Burke (or possibly for Burke directly). That will eventually lead to Burke being in a position to pressure Maya subtly, then more overtly. It will eventually lead to some sort of crisis, which will then be dealt with in Season 4. That's when I expect our heroes will finally put all the pieces together, realize the full scope of Burke's operation, and decide how to deal with it.
In the meantime, we'll get different short-term sequences depending on our choices. If we fooled around with Jade then broke up, we'll get lots of glares and snippy dialog with her. If Stephen has the video of the MC with Jade, he'll be bolder and make lots of veiled references to it. If we bullied Tybalt, we'll get some accusatory dialog from his parents, and probably some scenes with Tybalt as well. If we're on the throuple branch, we'll get to put in a good word for Maya, and maybe have some interaction with Josy on the side. That sort of thing.
In all cases, we'll have plenty of time for Maya to worry about the threat, then worry about being able to be a good intern, then worry about her father finding out too soon, then worry about whatever Burke winds up doing. We'll get the full dose if we're on Maya's path, but I suspect we'll get the highlights no matter what.