I can understand your point of view, but you have to ask yourself "what is real?". Yeah, cameras are getting better and better, but there is has not been the camera made yet that can fully capture what the human eye can see. I haven't seen the article you are referring to, but I can imagine that since you refer to the moon and bats that it would be almost the worse case scenario for a camera. You have low light, yet you also have a bright light from a moon, and you have small MOVING critter. The human eye can see all those things at once, but a camera can't. So you do have to ask "what is real?" what your eyes see, or what the camera is limited to? I personally lean towards what you see. So, photoshop and other programs are simply tools to help show what your eye sees. To me it's kinda like black and white. Would anyone say Ansel Adams is a fake because he shot black and whites? It is simply a tool.
Now the wild vs captive critters are a whole different ball of wax. I don't have any problems with taking captive pictures. Most people will never have the opportunity to see certain animals in the wild. I can't remember the photographer's name, he's in this months OP, but he has a good write up on his web page about this whole deal. Basically captive photography is necessary. He uses wolves as an example. They are very rare in most areas, and in the areas where they do live they are very secretive. Most of the nature photos you see especially the den pictures are taken captive. These are the pictures that capture peoples minds and interest people in the welfare of the animals. With out using captive animals these pictures may never have been taken, with out these pictures people may never have connected with the animals, and with out people connecting with animals and being concerned we may never have saved them. Now with that said, someone should never try to mislead people by selling captive as wild. Someone that purposely lies and calls a captive animal wild is just wrong. The way I see it, and others might disagree, is that I don't care where it was taken. You show me a shot of a wolf and I'll enjoy it whether it is captive or wild, I'm just interested in seeing a good shot of a beautiful animal, period.
Here's a link the that site I mentioned. http://www.naturalexposures.com/captivity-statement/