The whole attitude of the meeting would worry me - to some extent the lunch box is the least of it - in so far as he challenged you about the lunch box contents, you told him, he disbelieved you, instead of saying this just got the lunch box out hoping to humiliate you and prove you wrong but instead was proved wrong himself as the lunch box contained exactly what you said it did and was done according to the dietician's advice.
however, exactly the same is happening when you told them about your dd's symptoms. THey didn't believe you, told you what they thought, but this time - they stopped at the point that they had told you what they thought and that they think is the right thing to do - and this is still what they think is right. There was no lunch box to bring in to prove them wrong. Whilst they could have talked to your dd about her symptoms, it doesn't sound like they are listening, they are intent on following their beliefs regardless.
In your letter I would also include something about your dd's symptoms, that these are recognised symptoms of her condition and that you want to continue to treat them as the specialists have said, not to follow their 'advice' as you believe that this will harm your dd and set her back in all sorts of ways (ie for the incontinence things - not just because she can't feel the need to pee, and that stopping wearing pads will not make any difference to this, but that given that she will then have accidents, it's going to put her at risk of being teased and bullied by other pupils. It's also embarrassing even if she does have nice understanding friends. And it's not very nice in the class if she does have an accident, somebody needs to clear it up, it's not her fault but doesn't make it any nicer.)
I would try to make sure that you get the last word in about your dd. So state what your dd's symtoms are, simply and factually. Say what the specialists have advised doing about this (and/or specialist resources such as the EDS conference or support group etc, think there are several people on here that have it and could offer advice too). Then set out what school is suggesting. Then set out why you are ignoring not taking their 'advice' but will be following the specialist advice. If possible do this for each symptom. If your doctor/any others involved in your dd's care are friendly and you think would back you up and disagree on the suggestions made by the school, I would cc them in too.
Could you also put something in the letter to say that you were disappointed that despite the fact that your dd has been at the school for xx years, they still do not appear to have educated themselves about the condition she suffers from, but instead have just made assumptions based on normal non-EDS children and made up their advice based on this rather than actually knowing what they were talking about (obviously this is maybe slightly too harsh a wording!), so there is something in writing in which you are showing that they don't know anything about your dd's condition and yet are happy to offer advice that can be detrimental to her rather than actually finding anything out.
I have a friend with EDS and her dc also have it - I know the struggles she has had and that's at schools that have tried to be understanding and accomodating of the dc and their problems. Must be complete hell when they don't bother to find out anything about it and strut around thinking they know best, when actually they don't. Good luck!