The first time you see Shady (for him) in bk3 MC says "Shady! youre here" Shady: "Do I know you" MC: "We will" Shady: "I like that, Im going to use that line" paraphrasing it because I dont want to get the exact text but it should be close enough. So if Shady is jumping around too that means he intentionally pretended that bk3 was his first meeting to throw you off. But that also makes the Shady is MC theory weird if Shady wasnt pretending there, thats why I think if Shady is MC he has to be split. Shady didnt get all the memories so its like he knows half the story.Naga has little regard for timeline, it seems just an option for her. If Shady is somehow snakish spirit, I see no problem with him appearing seemingly later and then go back just as MC does.
I feel like Im doing a bad job explaining, this is like some doctor who shit where some spoilers here but when the doctor meets his wife for the first time its her last time meeting. And for the doctors last meeting its her first meeting. The doctor and his wife experienced their timelines in complete reverse, his 2nd meeting with her was her 2nd to last meeting. Time travel makes all this confusing I wanted to be sure which event he meant.
For the timeline theres several events that happen in bk2 that they show were caused by bk3. Thats why the girls didnt get along in bk2 but they were together at the start of bk3. The events of bk3 caused them to drift apart.