Hehe... be honest, is it more like a failed attempt at a whistle?
If so, that would be a hiss. And that would explain why it only happens when he's out. Just nervous (or as you've mentioned, feeling threatened)! Does it also stop after a few seconds/minutes?
That's my guess, apart from the issues you've already mentioned!
(Quick question in return: how long have you had your ball python?)
P.S. I'm not sure how much you've read about snakes in general, and I do not want to ruin your day... but snakes do not love anything - or that's the popular opinion based on the science known about their brains. They are not social animals, and do not really even "like" us! They tolerate us, they allow us to hold them, or what not. I do think they can prefer certain people to others, as in, they have associated one individual with warmth or security or even food. But I think that's about as far as that goes for them. And they can't help it! Once we accept that, they are that much easier to loveme thinks.
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