Am no expert by any means, but Pepper does the same thing. She's fine as long as there are no doors shut between her and whoever is in the house. As far as we know she's ok when we go out (no complaints from neighbours and I have asked..) She is more than happy to be in a completely differnt room.. by herself or with my other dog, as long as she knows she can get to the person.
What I have found is that if we want to shut her away she settles much better if given something to eat ( a few biscuits in a kong, a pigs ear, something that takes a while to eat - frozen meat and biscuits in kongs work best) Once she's eaten, rather than whine she goes to sleep. Might give you a starting point, say have him with you in the morning then pop him in crate with kong/food toy ( I used to have a brill one by busy buddys, looked a bit like a UFO) and leave for a while after the food has gone. You'll need to work on the length of time, but am sure he'll get the idea.
Once he's twiged that crate means being left but with food, then vary the times you do it (say put him in with breakfast for a few days, then with tea) so he knows it's not just at lunch time
