The survey says nothing about how strongly folks hold that preference. I may prefer Schwepps Ginger Ale, but I'm not going to be irritated when offered Canada Dry instead. That "40-60%" number is a ceiling, not a floor.
The reasoning seems sound though. Where there is no strong user preference, consider making it configurable.
The only way you find out how irritated people would be without the option would be to piss them off.
Those users who like the sane defaults can just stick with them. Those users who don't like those defaults can use the configuration options to fine-tune their experience.
IMO sane defaults and extremely detailed configuration go against each other. The detailed configuration makes it impossible to find the option you want.
Emacs is nothing like Eclipse. If anything, I would compare Eclipse to Vim: bare bone its useless, with plug-ins its just too big and unstable.
:)