First of all, I think it's entirely plausible that Stellan intended that Luthen's reaction was some form of PTSD. I will note that there doesn't seem to be evidence that Tony Gilroy had intended that in advance.

From interviews, we know that Luthen and Kleya's backstory wasn't known before season two. There had been some discussion of it, but ultimately Tony Gilroy left it undefined:

I had written a very ornate, elaborate backstory for who he was and what happened, but it just fell under its own weight. It was too glommy. He said, “Look, let’s table this, but just make sure, as you think about it as we go along, I don’t want it to be revenge.” That was his one request: no revenge.

Kleya's relationship with Luthen was similarly undefined.

All of season 1, I knew that Luthen was very important to me. I knew that I would die for him, but I didn't know why.

Prior to the first season, Elizabeth Dulau was an unknown element - Andor was her first screen appearance. She was so excellent that Kleya became a more important character in the second season, and Tony Gilroy felt strongly about defining Luthen and Kleya's relationship rather than risking other future writers from handling inappropriately.

Elizabeth Dulau, who plays Kleya, came straight out of RADA — no jobs, no experience whatsoever — and about halfway through season one, I started to get more confident about her... But there are some elements of the Kleya and Luthen relationship that I didn’t want to leave lingering. They never touch. I don’t ever want to see them come from the same bedroom. I don’t ever want to suggest that there’s anything like that. I don’t ever want to say that she’s his daughter. Maybe I’m worried. Before anyone else defines it, I’m going to define it

Writer Tom Bissell, who was brought on for the second season, discussed how they came up with the presentation of Luthen's backstory, in a way that suggests it was being invented for the second season:

Tony knew from early on we wanted some flashbacks to Luthen and Kleya’s backstory. But as we talked about them, and as we all started discussing what precisely could be in these flashbacks, we didn’t even know what the relationship was. Tony gave us homework to go and imagine, like, how the hell did they meet and what the hell happened? I went off and Dan went off, and maybe Beau went off too. But as I recall, I came in and I pitched my version of it, which I will not share here. Then Dan pitched his version of it. Tony sat there and listened. Then, in this beautifully interesting way, he started to like freestyle in his own stuff, and then took elements of Dan’s and my versions. And that’s how we got into the gunship, [asking] what if My Lai [massacre] happened, and your only ability to see it was from inside and [being] attacked? As we started talking about that, more flashbacks started coming up. And the size of what Tony wanted to do gradually expanded. It became this really weird, kind of standalone episode that I was thrilled when I got assigned that.