My personal theory on the season 4 finale
This focuses primarily on Skip's outburst monologue, with the idea that skip was talking in code the whole time, with only McGrath seemingly catching on.
The way skip begins the conversation feels very similar to the conversation he had with McGrath and Athena that was done in code, both having variations of Skip talking about 'really listening', with him having a large amount of emphasis in the scene.
During the ran Skip says 'Do I even know semaphore McGrath?' I think this is his way of trying to 100% confirm the code or continue the code on because semaphore is a method of silent communication with flags, and I honestly believe that Skip would know semaphore
In the scene, they were all being listened in on by Terry Millionaire, and everyone knew that, if Skip did have something he needed to communicate to the team, he would need to do it covertly, through some sort of code.
Given that Skip resigns at the end of the monologue, McGrath seems incredible calm about it, especially considering her reaction to Skip attempting to leave the EMF on the American Spydol mission. I don't think she'd do that if she didn't know what was going on. Plus, despite his resignation and things he said during his outburst, she still said 'I'll see you around', meaning she doesn't think this is the end for them, and doesn't even sound remotely concerned
Finally, despite the things Skip says mirroring his feeling from throughout this season, and I can imagine that he is absolutely hurt by everything that happened with Gloria and the promotion, I don't think Skip would be so aggressive just because she kept it a secret. Yes it would hurt him, but going to the extent of not calling them friends, only coworkers, after all the time together, it just didn't feel right. At this point he still admitted that he thought he could help Athena become good despite already knowing about the lies from everyone at that point. He may not be completely ok with what's happening, but Skip understands how compromised they are, and realises the only way to deal with this is from the inside.
I don't know though haha, this is just a theory, and may just be me trying to hang on to the dynamics and relationships skip has created, but I feel the theory has some backing to it.