So playing devil's advocate (I do think there's way more evidence that Marina hasn't been complicit since the start, so this is imo highly improbable), there are some possible explanations for some of her confusion and anger.
- The initial anger at Andrew committing to being Elena is just her lying. She travels to isolate Andrew.
- Her meeting Roan is a lie and the flashback we see isn't what actually happened.
- Her being surprised when she next speaks to Andrew is more acting. And her leaving just in time so that the Doctor goes too far with the surgery was pre-planned, with the flashback showing James showing up another lie.
- Her getting upset about Elena not responding to the passphrase is because she's concerned since Andrew shouldn't be ignoring the passphrase. She's wanting to see Andrew fully immersed in the role while also being terrified about the mob plot.
- Then, she sees Elena is planning on marrying Nikos and is sleeping with him, while also ignoring the passphrase. She believes Andrew's happy, which isn't part of the plan. Which makes her even more upset.
Now, there's some major signs this isn't true. For one, I think the fact that Marina originally kept referring to Elena with the name Andrew even after all the surgery was a big sign that she wasn't trying to force him down that path. Otherwise, she would have directed the conversation to play up the whole "scary mobsters are looking for Andrew". Similarly, after the time skip when she keeps being resentful towards "Elena", if all of this was meant to be to spite Andrew, I'd expect the inner thoughts to be either referring to Andrew, or to be sarcastically calling her Elena, rather than seemingly playing it straight.
Also, Nikos is the one that instigates the feminization plot. So for Marina to be wanting to feminize Andrew, she must have worked with Nikos.
This means there's two problems/oddities with Marina being part of the feminization plot.
1) If the plan was to fuck over Andrew for Marina's sake, than Nikos should be directing Elena according to Marina's wishes. Which clearly hasn't happened. Now, one could argue that he's now backstabbing Marina. If that were the case, than you'd think Marina would have had a stronger confrontation towards Nikos.
2) If she is really working with Nikos, then there should be minimum surprises. While you can argue most of the things Marina says are explainable as part of gaslighting Andrew, I think scenes like bringing up Filip's disappearance and reappearance make no sense in that context. If Filip's just part of their plan, then it's super weird that Marina brings it up without directing Andrew to do something with that information. Seems more dangerous to leave a loose end like that.
