I agree. Focus on how his behavior impacts your child's medical or psychological issues, including how this might impact your relationship with the doctor. And try not to judge your ex for these things, and the doctor will probably understand. If communication with the doctor in the presence of your BPD ex is an issue (this was for my DH and his ex), then explain that using terms that do not point the finger: "We have a history of high conflict in our marriage, and this makes communication about our child difficult. I would prefer being able to communicate with you directly without my ex present if that would work for you."
If you have psychological concerns, I think it is fine to specify what they are, too. Particularly if your child has been subjected to physical abuse or witnessed abuse. These are important things for a doctor to know.
Whatever you say, make sure you are prepared to have it read out loud in court.
And strategize. Maybe you look at this as a year long thing. The first time you mention it to the doctor, say that you and your ex have very different ideas about when to medicate the kids. Second time, add more info. Third time, point to your experiences, documented.
Make the doctor a sympathetic partner in your concerns, which is to do what's best for the kids.