This article is interesting in that is speculates that bearded dragons maybe particularly adaptable for captivity as quantified buy stress hormones of captured wild dragons. My interpretation from this and anecdotes from wild dragon observations is they just don't give a flip. Certainly naturally being more tolerant of stress makes them a more tolerant pet than something sensitive like a chameleon or some of the exotic species.
A little off topic but
this is also a good article that discusses the importance of enrichment. A stimulating environment/lifestyle is just as important as heat and light for keeping animals both physically and mentally healthy. A few of the linked studies show how enrichment can help the brain and mental resiliency of reptiles which in turn would make unnatural circumstances like handling and being pet less stressful for them. I also prefer a naturalistic approach, but enclosures don't necessarily need to be "natural" to be enriching. I really like the woven grass hammock/ladder I got recently, and there are many clever things that can be done with bricks, tiles, shelves and boards to make a habitat better.
Lastly I want to emphasis a point made by Rankins. Especially with how different reptiles are from us the line between tame and learned helplessness may be even harder to recognize for us. Learned helplessness is the concept that if an animal (or person) is prohibited from avoiding an unwanted stimulus enough, they just give up and eventually won't even try to run away or avoid it. This is one of the reasons I don't like the idea of forced handling (restraining the dragon or otherwise forcing it to interact with its keeper when it doesn't want to)... its not really teaching the lizard to like you, its teaching them they have no choice but to go along with it.
Our understanding of reptiles capability for learned behaviors and their own natural ingenuity is growing, I'm sure our understanding of their 'emotional' lives will too eventually.