Are you sure he wasn't trying to nose bonk you for pets or to get your attention for something else like food? Nose bonking is how rabbits let us know they want something from us without resulting in nipping to get our attention, which of course nose bonking is a much preferred method for them to communicate with us.
If he was making circles around exploring, him nose bonking you could have also been him trying to say you were in the way of him trying to explore or run around. Which would mean he feels perfectly comfortable with you or he wouldn't approach you for a nose bonk at all. So it's not necessarily that he may not be comfortable with you. If he wasn't nose bonking you as a request for pets, then it could be that he was busy wantinng to do other things right then and was requesting that you move so he could get past you.
Some rabbits are just very active and busy, and with these rabbits the best time to interact with them is when they've worn themselves out exploring and lay down for a rest, then that's when they will usually be more accepting of head rubs, but only if he's to the point where he feels comfortable with you approaching him.
When he's laying down, slowly approach with your hand in his field of vision(not directly in front of his face or behind his head). I'll hold my hand near their nose so they can smell my hand first, then if they don't move away I'll give a gentle forehead scritch. If they stay there, I'll keep giving them gentle forehead rubs. If they move away from you, then they aren't quite ready yet.
If they hold still and don't move away when you try to give a gentle forehead rub, then it means they likely are accepting of it and want you to do it, especially if they then lay their head to the floor or push their head under your hand and hold it there. That's basically them saying 'yes, please' to head rubs.
Head rubs usually means start on the forehead between the eyes. That's usually their prefered place to be petted. Some rabbits won't like you touching their ears, cheeks, or petting along their backs, especially around their rumps. So start with the forehead when your rabbits are ready and don't move away from a gentle scritch. If they do move away from your hand, it can mean they aren't ready yet, or can just mean they're busy looking around and you need to wait until they're tired out and are ready to settle down for a rest.
If your rabbit moves away from forehead rubs, then it doesn't mean he isn't starting to become comfortable with you. If he wasn't comfortabe with you there at all, he would more likely have stayed at the opposite end of the enclosure away from you, trying to keep away from you. But just the fact that he is hopping around exploring with you there and nose bonking you, means he is starting to feel comfortable in your presence and is comfortable enough to approach you and touch you with his nose. The more time you spend observing your rabbits and their behavior, the easier it will get to start understanding and interpreting their subtle body language.
With Rex being reluctant to enter that room, some rabbits are just more cautious about new areas. Rabbits have established mapped out areas in their head, that they consider 'their' territory. Rex may consider this other room your territory and he is just waiting to feel more secure and safe before he gets up the courage to venture in. As he gets to be more comfortable with you and knows he can trust you, he will most likely start to feel safe enough to come into this other room. But then some rabbits are just more reluctant to explore new territory, even when they feel perfectly comfortable and safe.
A rabbit in loaf position doesn't necessarily mean they don't feel comfortable and safe. And them going to their pens to rest doesn't mean this either. Rabbits will go to their pens because they know this is their established territory, so it's their comfort zone.
The resting loaf position can be due to a rabbits body temperature, and doesn't always have to do with how comfortable they feel. When a rabbit is feeling too warm and wanting to cool down, as long as they feel safe they will be more inclined to lay flopped out. A rabbit that is feeling cooler in body temperature, will be more inclined to bunny loaf to help conserve their heat, even if they feel safe in their environment. Then there are some rabbits that just prefer to bunny loaf no matter what, even if they are a bit warm, and even when they feel perfectly safe. I've had rabbits like that, that rarely ever liked to completely flop down, though they felt completely safe in their environment. So you'll get to know and understand your rabbits individual personalities and what is normal for them and what their preferences are.
