There are reasons for a lot of the things in the game, but sometimes it's just "because it's only a game not real life."
For the food and bowl stacking, I don't know that I understand the exact situation, but it might be like something I still find confusing, although I basically understand. Some things that _can_ stack don't stack automatically because of differences in attributes. Food, for example, will sometimes stack automatically, but if the age of the food isn't the same, it won't. But, you can force it to stack by dropping them on top of each other, and they will adopt a "worst case" (or maybe average? I haven't tested thoroughly, I feel like I've seen each) where they all get the same attribute, thus losing the better attributes/age that one of the stacks had.
Is that maybe the case with your bowls? I don't know if I've stacked bowls, but I would immagine, like you, that the _exact same_ meat stew, bowls could stack. If it's a different stew recipe then they can't stack, because they're not the same item. If it's a state of some smaller attribute, like age, then I'd guess you can manually stack them as I found with food described above.
As to putting from bowl back into crock, sure, in the case of the exact same thing being moved I agree. Add that to suggestions, they might take it. It's a reasonable suggestion.
A lot of these things where things that make sense don't work, are likely just best as suggestions. If enough people want them and think they're valuable, they may well be added.
...just my thoughts...