When storing or for that matter transporting my bolt action rifles I take the bolt out and place it in the case. My mentor asked me why? Unfortunately, I don’t have a good answer.
My reason is actually pretty simple. That’s what my dad did, that’s what my mom did, that’s what my grandpa did, so I do it.
Is there really any reason to leave the bolt in?
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When transporting bolt actions, I leave the bolt in. There are little parts and such, that would be better protected, and easier to not lose if they are in the gun.
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I have heard of people losing bolts that way. 
Also with all my firearms when they are unloaded I pull the trigger so as not to leave them cocked in storage.
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Interesting question; I’ve never thought of that. I’ve only got 1 bolt action, and the bolt stays in, but open. Maybe it’s from some point in history where bolt actions under hard conditions would rust shut? That’s just a guess.
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I’ve known folks to do that and I want to say I read someplace (airline mebby) that said transport with the bolt out but I can think of no good reason to do it unless the bolt interferes with closing the case. I am with @BRUCE26 for keeping the bolt closed and dropping the hammer on closing to keep random junk out of the action. From the great magazine loaded or unloaded debate we know that it doesn’t really help the spring “relax” but having the firing pin forward closes up another “hole” that dust bunnies and such can crawl into.
Cheers,
Craig6
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Being a lefty, I have avoided bolt action rifles like the plague. When I case my autoloaders bolt is closed and hammer dropped on an empty chamber.
I had to bring some Garands to the Springfield Armory for repair and they wanted them delivered cased or boxed with the bolt locked back.
As far as the bolt in or out. The dust bunny and lubrication issue tells me to leave them in and closed.
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I suspect this is only to make sure that someone is not sending them a loaded gun. Wonder how often that has happened?!
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I don’t think there is a right or wrong answer. I keep the bolt in. As mentioned above, possibility of loosing the bolt, or if it is not properly cased, the bolt could roll around and ding the gun up.
If you keep them like that in your safe and have my luck, you might grab the wrong bolt when you take a gun with you… 
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When transporting a bolt action rifle or even a hand gun I have put a cable lock or padlock on the gun. I place the bolt in a small case inside the locked gun case. This makes it less ready to access and use.
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Ruger gunsite…308 available for lefties
Personally, my 3 bolt guns get a spray of ballistol on the bolt, then it’s closed.
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Thanks for the info. I’m not in the market for a long gun at the moment but, never say never! 
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Yep! Ours are ceremonial set up for blanks but they likely as not got some surprises!
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Do whatever works best for you. BTW, I think your method is fine. You might consider putting the bolt in a bag or case while it is being transported/stored.
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