Many of the checks are stylistic.

Others could have adverse affects in code, for example, `trailing` throws an error if there is trailing whitespace, which can cause issues with regex and can be a pain to debug.

`indent` could be argued to be enforced by coffeescript, as well as `eqeqeq`, which enforces using `===` as opposed to `==` (Coffeescript's equivalent is the `is` keyword).  It looks like Coffeescript has a rather different behavior for `for in` than what you'd normally get in JavaScript (it doesn't actually use it).  I suppose you could count it though.  You could also argue CoffeeScript covers using `strict`.

Some things are just different, and both JavaScript and Coffeescript have their own unique gotchas: http://raganwald.com/2013/07/27/Ive-always-been-mad.html
That's one of the reasons Coffeescript is being linted too.

I really don't want to go through every single option line by line since there's quite a few, but you can read up on all the options at http://jshint.com/docs/options.