Those reactions, closing eyes, lifting head, etc... are all defensive mechanisms.
Especially in the case of the eyes closing. It is their way of saying "if I close my eyes, maybe it will think I am dead and go away".
There was some research done a while back, specifically in Iguanas, that went through these types of things. Most reptiles dont have the ability to run away quickly, especially when they are in our confines, so they have a number of of these defense mechanisms.
I am sure that if one searched enough for it, you coudl find plenty of info about it.
To be clear to all, these responses are another example of us applying our human emotions and proclivities onto these animals. "When I feel relaxed I close my eyes and enjoy", this must be the case for my chameleon as well.
All the time they are terrified of it.