Everything is negotiable. Some things are just easier than others. Besides, did you tell them up front what was negotiable, or did you just kinda expect them to figure it out?
Here is the thing - the company would have zero difficulty with me asking for a $100/day per diem while traveling for months on end, instead of doing expenses - that was negotiable. But there was absolutely zero chance of getting a $7 bag of cough-drops allowed as a medical-expense. Non-negotiable.
(The thing is - when doing expense reports - it usually was pretty random which line-item you grabbed for some things - there were two or three categories that might make sense. Not so with that medical line item).
Money and equity are easy to negotiate because there's no management overhead. But if you want your 401k to be at a different brokerage, or have other "process" request like that? Probably not gonna happen - not for a line employee.