I think you are looking at this from only one angle. There are definite uses for granular control over page HTML. Just because there is little/no use in such functionality on 99.5% of all WordPress powered sites doesn't mean that it should be discouraged.
I still don't get how on earth Carrington helps with this, but hopefully it will all become clear in time.
Hardest thing for me to do in a theme is to add code from plugins into the theme so that the plugins output displays where I want it. I need to know where the loop is and place code within this special section of code. If I don't want this edit deleted during a theme upgrade, I need to add the code to functions.php.
Dan Coles plugin looks like it could help me with this problem but that's been the hardest issue with themes for me.