Actually, thinking about it, stockpiles and beds are the perfect example: A bed room derives its function from its name giver, the bed. No bed, no bed room. Thus it makes sense to have the bed as an integral part of the bed room - a bed room without a bed makes no sense.
A stockpile, on the other hand, allows using bins or barrels, but they are not an essential part of it, but can leave it at a moment's notice. Even without any furniture, a stockpile is still a logic thing as it really just means the space open for it.
This sounds logical according to the way bedrooms currently works in DF. However, I agree with Jiri Petru that DF would be easier to to play and make more sense if some parts of the game (like bedrooms) worked differently.
For example, there could be many benefits from being able to assign an empty room to a dwarf. Even if they have no bed in there, they could still go there to sleep - sleeping on the floor in a private room of their own should be preferable to sleeping on the floor in a hallway somewhere. They could also store personal items in their room, with or without chests or cabinets, and conduct private meetings or discussions when that kind of things becomes more common and interesting.
Right now the bedroom is basically the home of an individual dwarf and many activities takes place there. I don't see it as necessarily obvious that it *has* to emanate from a bed. If you happen to settle somewhere without wood and can't make beds, I think it would make perfect sense to still be able to give each dwarf a room of their own.
You could argue that this kind of reworking of existing systems wanders outside of the topic of interface and presentation - but
if it's impossible to make a consistent and sensible interface to describe and control the way the game works, the game should be reworked as well.
I love the Jiri Petru's idea of redesigning room construction in general to follow the hospital model - designating each room or work zone first, then placing furniture as needed. It makes a lot more intuitive sense to decide "This should be the dining room! Let's get some chairs and tables!" than to decide "Here's a table! Let's all eat our dinner in this general area". It would also improve workflow when carving new spaces - you could designate rooms of different kinds even if you haven't yet built the furniture required to make them function, making it easier to remember which was supposed to be which later on.
Anyway, awesome cool discussions in this thread so far.

I hope Toady reads it and some of this makes it into the game.