2.5 yr old puppy growling at owners - Training tips?

Our dog has gone through training, and is very well behaved, but we have 2 instances when he growls at us. Currently we are backing off in the instances below, but are not sure how to proceed in correcting this behavior. We use positive reinforcement and clicker training, at least up until this point. Any advice is greatly appreciated.

1. He growls at us if we try to pet him in the morning, in our bedroom. While we get ready for work, he seems upset/stressed at us leaving (no that he has learned our routine). If we bend down to pet him and reassure him, he gets still, the whites of his eyes show, and he growls. We always back off when this happens. This happens if we sit, bend over, or any approach. The room is his sleeping area (we started him in a crate in there, and now he sleeps on the floor). We know that he is perhaps stressed at us leaving, wishes to be left alone, and may be guarding his "bed" area. But, we think this is a behavior we should work to correct as if we have visitors, the last thing we want is for him to growl at us. Any suggestions on training tips to correct this?

2. Food/resource guarding. Our dog is very good with toys and food until we give him a high value item like a real bone from the pet store. If we walk by or even move our feet while sitting on the couch he goes stone still and starts growling and showing his teeth. He is the only dog in the house and we never try to take away his treat. We are not sure why he started guarding or being so sensitive to any movement and would love tips on how to correct this so he doesn't growl anytime we move in the same room with him.

Thank you!!!