1 stomach unit does not necessarily equate 1 energy/hydration unit, these are three separate units, some foods may take more stomach space then others while providing different amounts of energy or hydration. So in general losing 600 energy and 1000 hydration doesn't really mean you should also empty 1,600 stomach capacity.

As for not being able to digest food while having the vomit status effect, it might be intentional, how long does it take for the 'vomit' status effect to disappear? Does vomit induced from different sources incur different penalties? i.e, I can understand why vomit induced from food poisoning would keep you nauseous for a while after you've vomited however this shouldn't apply to vomit induced from over-eating/drinking.

Just my thoughts on the matter.

I understand that it doesn't necessarily mean the same thing, but 600 seems to be too less.

There is no "vomit" status effect, if you eat/drink too much, you vomit once, get the "sick" status effect, and be done with it. After that you don't vomit again unless you eat/drink too much again, at least in my experience. Haven't tested other sources of vomitting.

The problem is just that if you vomit a few times in a row, you will become hungry, thirsty, AND full, making you unable to saturate your hunger and thirst.