Using the crate for a time-out is not the same as using a crate for punishment. When you put the dog in a crate for a time-out, you wordlessly and unemotionally take the dog, put it in the crate, and leave. When the time-out is over you wordlessly and unemotionally return to the dog, let it out of the crate, and continue what you were doing before the time-out occured. The dog is not commanded to go in the crate, it is not yelled at - nothing. That means there is nothing negative to associate with the crate.
When you use the crate for punishment (which you should never do), you yell at the dog, put it in the crate, yell some more. Lots of negative associated with the crate.
Sit-stays and down-stays may work in some situations, but may not be powerful enough for the dog to really get the message. (And if you're working with a puppy who hasn't learned stays yet, they'll be totally useless.)
Julie