There's also the mental cost of navigating among all that commented code every single time you need to read that piece of source.
In the event it is needed to be glanced at or restored, but you're exaggerating how problematic commenting a method out of code is. If I'm scrolling through code and see a commented out method my brain says "well that's not in use" and I move forward.
If a commented method stays in code for a few months I would complain or simply remove it myself, but it isn't hurting anything (unless in the case of Ember).
I can't think of any reason to do it that isn't a half-assed attempt at something a good source control system does much better. If you have lightweight branches, blame, and logs you can search and check by date, along with good changeset comments, then you already have everything your commented-out code can do, and all in the same place and system, instead of spread out into several different systems.
As far as Ember's issue, we didn't see the actual code. There's almost certainly a misplaced pointer somewhere. The author made of not being a JS regular, my guess: missing `var` somewhere.
However, commented out code is by definition free to be deleted by anybody else if it happen to be forgotten later on.
You may also want to check out FUSE (http://en.wikipedia.org/wiki/Filesystem_in_Userspace). Something on top of git may already exist. If not, it wouldn't be too difficult to create something like that.