If the therapist does not insist on talking to both parents, that should raise a red flag. If you can, be sure to talk to the therapist on your own so you can share your thoughts. You can be diplomatic
How does your wife respond to validation? It might be important to validate that she is concerned about your son (no need to validate whether he truly suffers from anxiety).
It's also possible that she is extremely hypersensitive and attuned (this is true of the BPD people I know), and can sense your son's growing anxiety about being alone with his mom. My son learned at an early age to become who he needed to be in order to appease his BPD dad. He was a happy kid, but he began to realize that he had to take care of his dad's feelings, which reversed the natural parent-child role, in which the adult is supposed to provide emotional reassurance for the child. That can be very anxiety-inducing for a child, who lacks the skills to take care of a parent's emotional needs, yet tries to do so nonetheless.
Let's hope the therapist is good, and insists on doing a round of tests that are objective and not based on second-hand testimony from one parent. My son's psychoeducational testing was extensive. It involved 6 hours of testing with S15 (9 at the time), two separate hour-long in-person visits with the therapist (we were divorcing at the time), plus a long-form multiple-choice objective survey that both parents filled out. Then 4 teachers did the same test. We received results with a diagnosis based on all that. Insurance paid for 75 percent -- it was expensive, but thorough and one of the most important benchmarks to track S15's issues.
The female teachers and I saw the same issues. A male teacher saw some of the same stuff, but to a lesser degree. He also saw a lack of leadership traits in S15, which may reflect what different genders see as important. With BPDx, it was like he was describing a different child altogether.
Lesson 5 on the Coparenting board has really good material about raising an emotionally resilient child when one parent has BPD. Since you are the non-BPD parent, it will fall to you to become the emotional leader, not only with your wife but with your child. I can't say enough about how helpful these resources were, especially the stuff about validation. Hopefully whatever therapist gets involved will not rush directly to medication and will instead focus on unpacking whatever issues might be going on, and help S5 develop skills to manage anxiety. Whether he has a disorder or not, the skills will help him so much as the child of a BPD mother.