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Yes, I would not use his safe areas for time out, so no crate for time outs and no to the gated area between the kitchen and utility room, IMO. You want him to feel safe and comfortable when he's in his crate and other dog safe areas when you are gone, and to understand the difference between time outs when he's done something wrong, and time when you need to leave the home and have a safe place for him.
As for the zoomies, we always just let our dogs run it out when they were puppies, unless they got too crazy, and then we just put them in their crates (not as punishment, mind you, just for bedtime). As you say, it's really about being over tired and not being able to really control that. So, IMO, there's nothing wrong with just putting him to bed in his crate when his zoomies are too crazy. Just make sure you aren't really reprimanding him, rather just putting him in his crate for bed.
As for the zoomies, we always just let our dogs run it out when they were puppies, unless they got too crazy, and then we just put them in their crates (not as punishment, mind you, just for bedtime). As you say, it's really about being over tired and not being able to really control that. So, IMO, there's nothing wrong with just putting him to bed in his crate when his zoomies are too crazy. Just make sure you aren't really reprimanding him, rather just putting him in his crate for bed.
