We have a similar arrangement - joint stuff 50/50, with some individual purchases.
First, in general, it can take some time to work all this stuff out, so you both feel okay with the plan. Also I like to look at the big picture - savings rate, and increased saving/spending within marriage. So for us, we're at around a 50% savings rate, so I don't really care about budget tweaking. And although if I was unmarried I might be able to spend less on food, among other things, I'd spend more for housing, so it probably all balances out. I'm also willing to pay a certain amount to keep my partner happy. I don't want to nitpit his choices.
But for the specifics of your questions:
Grocery food - generally all split 50/50. He has some expensive things, I have some expensive things. We generally agree on organic food choices. He knows my gluten-free is medical, not just fad. I know that convenience is more important to him than cost, as he works a lot. It's definitely not worth it to try to figure out exactly what portion the other person eats. However, if it was widely one-sided with expensive food you have the option of negotiating a different percentage in that category. Maybe that's an option for you. Some food is individual - if i buy snacks just to eat at work, and his daily coffee - that's all individual.
For individual meals out, he was eating out a lot for a while, so we decided to consider half that cost as "grocery", as otherwise he'd be eating food we bought together, and half personal spending.
For supplements, we consider these individual. The only thing I know 100% works is my glucosamine, which is kind of pricey. But then we both get on vitamin kicks as well, so any non-shared vitamins/supplements are individual. I'm just used to splitting these out of the receipts.
For prescription drugs, however, we consider those joint, as you can't completely control your health. I thought this showed a supportive environment just in case one of us became seriously ill. I wanted to set the precedent of splitting this.
So that's my thoughts on trying to figure out if this battle is worth it, and what we do in my marriage.