I’m not trying to cut the other parent out of major decisions. Ideally, I would like both parents to be involved and for decisions to be made cooperatively. The issue I’m running into is that when my ex gets upset, she can make sweeping decisions on her own, change the schedule, withhold cooperation, or frame unilateral choices as being in our child’s best interest without actually including me.
My sister has a highly contentious divorce and parenting schedule with her uNPD, high-conflict, non-cooperative, dysfunctional ex-husband. I see you're considering potential issues around non-cooperation and unilateral decision-making, which are exactly the sort of things you should be considering. However, no matter how much you try to establish the legal "rules," that doesn't necessarily mean they'll stick to them in practice--because BPD/NPD often means being governed by emotions and not by fair play, and typically not in the child's best interest. That's why you need to document everything, in case you need to go back to court.
Anyway, in practice, I think it means that when your child is with you, you proceed with your normal parenting: taking your child to the doctor, taking him/her to activities, monitoring screen time, doing homework, sharing meals, etc. If your kid needs to go to the orthodontist, I'd say, just schedule an office visit during your parenting time if you want to ensure the orthodontist visit actually happens. Ditto a visit to the pediatritian. If your kid wants to play soccer, then you go ahead and take your kid to soccer practice during your parenting time. Maybe mom doesn't want to deal with the hassle of soccer practice, and that would be a shame, but at least your kid plays soccer when they're with you. You could put the activities and doctor's visits on the common calendar for record-keeping, and I doubt that any court would rule that a doctor's visit or soccer practice is detrimental to the child. Your ex could throw a fit if she wants, but as long as you do what's right for your kid, there's little she can do. I mean, how could she justify saying that going to the doctor is bad for the child?
One area of possible contention might be child phones, for example if one parent wants a 12-year-old to have a phone and the other one doesn't. I'd say, the child could have the phone with the parent (e.g. mom) who allows it, but when visitation is over, she leaves the phone at mom's house. Mom might argue she wants to be able to contact her kid while at your place, and you tell her, she can call when she wants on your phone, but she's not supposed to interrupt your parenting time. As for contacting your child while at school, she can call the school's office as has been done for decades.
Another possible area of contention is media use. An example is that one parent wants to abide by movie ratings (e.g. a 10-year-old wouldn't watch a movie rated PG-13 or R, or watch pornography), and the other parent lets their kids watch anything on devices with no parental controls. I think in practice, media consumption is difficult to enforce from afar. I think that you establish the rules for your house and hope for the best at mom's house. But if you find evidence that your kid is consuming inappropriate media at mom's house, you might try to document it and get the court to intervene. But the reality is it's costly.
With my disordered BIL, there have been some questionable parenting decisions, such as taking his girls (aged 10 at the time) to get their hair permed and colored in whacky colors, and also wearing age-inappropriate, suggestive clothes, such as high heels and the like. Though that sort of thing angered their mom, at the end of the day, it was just hair, and just clothes, meaning nothing permanent. Maybe you could stipulate in the parenting plan that there could be no body-altering procedures (e.g. tattoos, piercings, gender affirmation surgeries) without consent from both parents.
At the end of the day, what got the court to severely restrict parenting time by the disordered parent was a detailed CPS report. In it, the guardian ad litem detailed deficient parenting: inability to provide meals to the kids, not keeping child-friendly food in the house, unclean living quarters, evidence of verbal abuse of the kids (e.g. calling them whores and idiots), sleeping during most of the parenting time, inability to pick up the children in a timely manner (making them miss their scheduled activities), missing a material amount of parenting time with inadequate notice, car accidents/evidence of unsafe driving, parentification issues, etc. In other words, he was unable to fulfill basic parental duties consistently. Sure, he had a million excuses and blamed his ex-wife for all sorts of things, but CPS saw through all that eventually.