Apparently, ES6 doesn't need namespacing because each file is a
  separate module.
This is misinformation. As far as I know, only files that use export are ES6 modules. Without export, an ES6 file is just an ordinary script that has access to the global scope unless it is either wrapped in an IIFE or is transformed during a build process.
Revision (12 July 2016): Apparently, I corrected misinformation with more misinformation. As Kyle Simpson clarifies below, "According to the current spec, what makes a file an ES6 module is how the environment (node, browser, etc) chooses to load it, not its contents."
In You Don't Know JS: ES & Beyond, Kyle Simpson, a.k.a. @getify, states
"Modules do still have access to window and all the "globals" that
  hang off it, just not as lexical top-level scope. However, you really
  should stay away from the globals in your modules if at all possible."
Now to your questions.
[I]sn't the second way, i.e., creating a custom namespace with an
  IIFE, better than the first?
That depends on the environment in which your module is running. For example, in node, there is no Window object; therefore, in that environment there is no need to worry about your modules polluting the global namespace.
On the other hand, in the browser, Window is a global web API, and your module does have access to it. Technically, anything your module attaches to Window is not, strictly speaking, global; however, anything that is attached to Window is so close to a global that it is generally considered to be a bad practice to modify it except through Window's own API.
[H]ow do I avoid global namespace interference?
and
[I]s there a newer/nicer way of doing this in ES2015?
I don't know what the best practices are for dealing with scope in ES6. For the time being, I do the following:
- If a file is a module, it's top-level scope is the file itself, so I don't concern myself with global scope.
 
- If a file is not a module, I wrap it in an IIFE.
 
Source: You Don't Know JS: ES & Beyond
Also Recommended: ES6 In Depth: Modules by Jason Orendorff