The game also doesn't tell us that Dwarfs drink twice as much as they eat. The game also doesn't tell us that their will be thief, be it monkeys or kobolds. The game doesn't tell us Elves only like certain things. The game doesn't tell us that the stock accuracy is based on in game perscion(sp) by the dwarfs. The game doesn't tell us that the dorfs perfer their own bedrooms. The game doesn't tell us that the dorfs for the most part, like to eat together.
The game doesn't tell us that cat will collect vermin and bring it back to its own owner, which it chooses by itself.
But those things are part of the game universe. They have logical reasons expressed in the game universe. The behavior of the 'cook' command is not logical and is not part of the setting; it is an interface and an AI issue. It revolves around "secret tricks" where the player is left to discover on their own that the AI is crippled so (for no logical reason) seeds can only be recovered when brewing, milling, or processing, not when cooking.
Once a player knows about these bizarre behaviors, they can easily avoid it by not cooking anything with seeds, and cooking everything else. Of course it's a workaround for the game's nonsensical handling of food, and given the fact that it
is nonsensical it's not something anyone is likely to find out without spending a lot of time on the forum or wiki, but it's not a factor in the game for anyone but the rawest newbies, either, and it's only a factor for them because it
is utterly unintuitive.
You are implicitly acknowledging this, but saying "Yes, I know its current behavior is illogical, unintuitive, and makes no sense, but I like it because it
makes things hard." That is a bad reason. The interface should not be set up in order to be hard; challenges should come from things in the setting (hordes of locusts, say) not from a deliberately crippled interface. (Although, as I noted, it
doesn't make things hard. There is no actual management involved because there are no actual decisions involved. Cooking food that has seeds is currently a flat-out stupid decision, but the game defaults to doing it and gives no indication of that. Anyone who knows about the issue can easily avoid it by growing food that has to be processed first.)
You still haven't answered my main question, either. Seeds provide negligible food value when eaten. There is no logical reason why anyone would destroy all their seed crops. That being the case, it is
not a management issue -- the player isn't "managing" anything, since management requires actual decisions. It is a mindless and unproductive task. In fact, forcing the player to perform mindless tasks like turning off cooking for seed-bearing foods
takes away from actual management, because it distracts them from making actual decisions by forcing them to repeatedly press the "push this button to not lose" button over and over again.
How about a split. Somewhere down the line, we can choose to have certain like industry automated, for least player input. So you can concentrate on the parts you like.
Although this would make the game easier, and at times, especially for new or early fortress, less frantic game play.
This still misses the main problem. The fact that cooking destroys seeds serves only one real purpose in the game -- it is a booby-trap the interface and AI set for new players by having the dwarves automatically do something silly. Adding a "turn off the new-player booby-trap" button is a bad solution to this, because the people who most need it
won't know that it's there.
I propose an alternate solution. Have a 'preserve seeds' option in the kitchen menu which makes cooking take a bit longer, but preserve seeds as long as you have less than 200 seeds in stock (the number below which seeds stop being produced.) Naturally, it defaults to on for anything that has seeds. Then, people like you who want the fun of dwarves destroying seeds for no reason can just turn it off, without it booby-trapping the learning curve for new players.