Here's how I understand it - you got lucky on the outbound. Your 1K status is extended only if you're on the same PNR. Otherwise, tough luck. So that was great, but shouldn't have happened.
For the return, agent was right. Since GPU hadn't cleared, they were in Y, and get the Y baggage allowance, which is 1 bag, not 2. Only had the GPU cleared would they have gotten the C allowance. So offering you the C allowance because the GPU will likely clear is indeed a favor. Why did they give you 2 and not 3 bags? This one is a guess - PMUA offered 2 free bags in F/C, not 3. If you bought the tickets then, then you would only get 2 bags, not 3, in C. And the 3rd bag fee is indeed $200. If not, then I have no idea why they charged the 3rd bag, unless they were only extending the favor so far.