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Using a crate as a time out will not make the dog associate it as a negative place if you do not put them in it in a negative manner. If they are calmly placed into the crate for a time out, it will not harm their viewpoint of the crate as a positive. You can use a bathroom if you like also, but you run the risk of them getting into trouble in there.
I've taught many people to use a crate as a time out and it's never made the dog dislike it. I've also done it myself with lots of foster dogs. There's no problem with it, as long as you are calm.
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