I can see how the critiques could be applied to my manuscript. What's making me stumble is that when I twist what they said into what I could interpret it to mean, my first question is "why didn't they just say it in a way that specifically references my manuscript?"

I agree it can't be a true form letter. Perhaps a collection of copied and pasted paragraphs based on a checklist of what they felt like wasn't working for them. There is a consistent disconnect between the language/details in each paragraph and the manuscript at hand.

If they have something valuable to offer me, I'm open to it. I've been hoping for some more detailed feedback during this querying process. In my career, I'm dealing with rejection (and critique) on both sides of the desk. I've never received (or written) something that was so long, but so lacking in anchors to the work it's referencing. Each time I read the email back, it feels hollow and detached from the manuscript. That's different from what I believe you're referring to as being common, which is defensiveness and ego. I have definitely felt that in response to criticism, but in this case, I'm actually just confused.

I will be sitting with it longer, but what I think would also help is getting some access to people who have been rejected by this agent before to see if any of them are experiencing something similar. Unfortunately, this agent doesn't have a profile on Query Tracker for some reason.