She’s eluded to him pushing past her boundaries in the last sexual encounter. If she were to come out and say that she has additional trauma
I honestly don't think there is a right or wrong answer here. This is a tough situation for both of you to be in. The first person that a wayward betrays is themselves. They betray their own stated boundaries in a number of different realms. That isn't said to minimize your pain and trauma, but waywards inflict upon themselves all sorts of trauma too. That trauma looks a little different, but having been on both sides of this coin as a MH, there is trauma on both sides that at least in my experience felt/feels about equal in magnitude.
I think something important here to keep in mind is that you do certainly have compassion for your wife, otherwise you wouldn't be struggling with this to ask the group. In fact, I think it is not that you do/don't have compassion, but you are kind of wrestling with the "where/what line does my compassion for her begin to wane?" and that is because in this example, she put herself into a situation with man she doesn't really know. Thus is another one of the major fallacies that waywards delude themselves into thinking that they know the AP so well, that they connect at a different level than they do with their own OBS, which is why they get the feelings and rush of all those hormones that tell them "we are so compatible, I know them so well." The reality is that to the WS, the AP is just mirroring and manipulating them to hear what they want to hear, and that creates that false sense of "knowing them" because well...they are mirroring you...who by definition and default you know better than anyone else on the planet...so you are essentially obsessing over yourself, which is kind of textbook wayward behavior.
Anywho, I digress, your wife in her delusion put her physical self at risk with someone she barely knew (although she thought she knew him) and I'm guessing from the sounds of it he pushed too far past a boundary for her. So you as the BH are now conflicted because in a sense your wife was what some would call "sexually assaulted" by someone and that someone happens to be her AP with whom she willingly consented to physical intimacy with, but if she didn't consent, that is what we colloquially will call assault or even rape. I mean, I think that we accept now that even a married couple that has regularly and repeatedly consented to sexual activity can still be guilty of sexual assault/rape of their partner if there is not consent.
Again, I think what you are struggling with (and please correct me if I'm wrong, I'm trying to help with a different perspective) is the dual nature of being very hurt and traumatized by your wife's betrayal but also sympathetic and showing empathy and compassion towards her because her AP, her partner in the betrayal, assaulted her.
For a thought, change the scenario. Instead of her having an affair, let's say that in a different hypothetical universe she doesn't know AP, but that same man rapes her (again, I don't know any specific details that would lead to it, just a hypothetical). So your wife is raped by this same man and the only difference in the circumstances is that rather than being her AP, they had no previous relationship and she had not betrayed you in any way like she has. I don't know you at all other than what you posted, but your empathy and compassion would be off the charts. You and your wife would both be deeply traumatized by the experience and through no fault of either of your own, your marriage would be irrevocably changed, albeit in a different way than it has been back here in the real world where she cheated on you but may have been raped/assaulted by AP as well.
Here are my thoughts and I will leave you with this. It is a tough spot that you are in, but I think there can be two thoughts in your head at the same time. If you show compassion to your wife for this "pushing past her boundaries" that is in no way a tacit acceptance of the broader behavior and the circumstances she put herself in for that to occur. In other words, showing her kindness and compassion for this does not let her off the hook for the betrayal, which is really the larger issue which she needs to show you her compassion and understanding as you wrestle with the bomb that went off in your marriage. My other thought, and maybe I'm projecting myself here, is that showing compassion and being empathetic is part of who you are, but your rational brain is struggling with "hey now, this woman just metaphorically knifed you in the heart by having an affair, you can't possibly be willing to be kind to her about this" but your instincts/gut are saying that the right play is to do the opposite since you are by nature that person. I would say, give yourself permission to show some compassion here, but be clear that you aren't accepting of her behaviors that lead her there.
Last thing (I know, I ranted a bit), since you mentioned you are on an R journey, this boundary pushing is also something that you two and use to be on the same side. The two of you can be united in the front that AP is a dirty scumbag. That agreement is something that the two of you can build on slowly as part of R, so as fucked up as it may seem, this is an opportunity to put some building blocks in place for an R foundation if that is what both of you want and how you treat it.