The "gg" thing is kind of an interesting topic. While I am sure that I have told someone hey you played a good game in a in-person game, it's not something that I can recall doing after every game played. When I play games with my friends we don't just all say good game at the end, unless someone you know played a really outstanding game that warranted a response of this nature.
In this regard I can see how the "gg" can almost seem like a token gesture that maybe many people don't even really belive. I did play a game against an expert once and got totally trashed with him scoring over 500 to my 200 points. When I got the GG, I did not really feel like a played a good game and while it did not upset me enough to say anything, I don't think the person I was playing really thought I played a good game. I also don't think he was trying to be malicious.
I have now personally moved away from saying the standard gg and just started saying thanks for the game. For me it show thanks for the time that the player invested in the game, giving an acknowledgment that I was playing agasint another human being, without anyway for it to be misinterpreted as a jab.
There was a time when I was playing up to 10 games at once, that I started to take for granted the human element of playing on BGA. It's very easy to get disconnected and find yourself only thinking about your perspective. This lead me to some behavior, like conceding games early when I felt it was a waste of time to keep playing, without any consideration to how it might make the other player feel. Which is behavior I would never consider if playing a game in person.
At the end of the day, I don't really think what you did was wrong, there is nothing wrong with telling someone GG, I just find that, because it can be hard to convey intent online, I would prefer to stray away from using it personally. But I am also coming from this from the perspective of having played other online games with much more toxic communities then BGA(for instance played LoL's for several years) and where something as simple as GG is actually used by many people in a very degrading way.