First, you said "If she's well versed enough with Moclan physiology and biochemistry to perform a complete sex change, including fully functional reproductive organs, she's experienced enough to decide if the procedure is necessary". I am arguing that she isn't, as evidenced by she didn't even know the procedure was performed regularly.
That's not an ignorance of medicine, that in ignorance of their society. You're equating an M.D. with an xenoanthropologist.
Now you say that if she knows enough about other alien biology and physiology, then that is good enough? She may know some other alien biologies well enough that she might be able to do the procedure (and I would kind of hope she is knowledgeable about someone's). But she clearly isn't knowledgeable about Moclans, so none of this is a foregone conclusion.
Again, you haven't established that she doesn't know enough about Moclan biology to perform the procedure. You've only established that she's not familiar with Moclan culture, which is not a function of her job. However, it might be fair to say that she has no experience with performing a sex change on an infant in general, because that's clearly unethical.
It should also be pointed out that she's probably already performed an examination of the newborn to determine that she is healthy, as that is what you'd expect a ship's doctor to do when one of the crew has a baby. Any such check-up would probably include screening for genetic and physiological problems.
And if she doesn't know about Moclans, then I don't think we can reasonable say that Bortas has a full understanding of her capabilities when asking her in the first place. He is assuming she is capable, but she demonstrates a lack of expertise in her response.
There is nothing demonstrated in her response to suggest that she has a specific lack of medical knowledge, and the fact that Bortas would request that she perform the procedure would suggest he had reasonable confidence in her abilities, especially since he request that the Captain intervene with the doctor on his behalf, which suggests that Bortas does not feel that her response indicates any lack of medical knowledge on her part.
Second, "what medical condition would a female Moclan suffer from other than "being female" "? I don't know, and neither does Dr. Finn when she denies the procedure.
Presumption. She may well be sufficiently versed in Moclan genetics to determine of the DNA of the baby would result in any medical conditions, and she can probably perform DNA simulations to determine that even if she lacked familiarity. It is the future, after all. And, in fact, the issue of such genetic conditions is never even broached in the episode.
And I am not saying "being female" is a condition.
The Moclans were the ones who view it as a condition, and it is the only condition that's actually mentioned in the episode, which is why I brought it up.
I am saying that other conditions might indeed arise from having the Moclan equivalent of two X chromosomes. Human males have conditions that arise due to physiology and genetics that human females don't, but we as a species still need both to reproduce, so heritable traits that kill/significantly harm reproductively-capable males don't survive in the general population enough to endanger the entire male portion of the population. They can't, based on how sexual reproduction and evolution tend to work. But in a race that has two genders, but which only requires one to procreate, the other gender could have serious heritable conditions and not endanger the survivability of the whole population and in fact could conceivable lead to a population made of a majority of, but not entirely, males.
Here's the problem with that: You made the whole thing up. It may be theoretically possible, but it's not indicated in the episode, and it's unfair to hold the characters to task for not knowing or considering problems that you don't know exist in the first place. I mean, heck, did the doctor check to see if Moclan females emit a rare form of nearly undetectable radiation that only females emit? How neglectful of her. Get that baby a sex change before everyone dies of space cancer. See, I can make up stuff they "failed to consider" too.
I agree with you that the "message" is probably what should be most at issue here. I just felt the characters should be shown to be arguing from a perspective of knowledge and understanding, especially when they were willing to make it a legal matter. Again, it is The Orville probably just wanting to have a fun show with a light take on these issues.
The show can't possibly encompass the entirety of every subject they explore. If they were forced to do so, it would probably bog down the story with endless asides and muddy any kind of allegory they were trying to make. Worse, the added complexity would only give the show more attack surface for critics who want to pick apart every part of the story.