Your comments

It isn't a JavaScript object, because it cannot parse things like:
font_size: 12
It would be nice if it could, though.

What is seems to be is just JSON+comments but there is no reason for it to be in any format - it doesn't have to be valid JSON since that data doesn't need to be passed to anything other than Sublime Text.

In fact, since Sublime is written in Python, I am surprised that its config is not in YAML which is a clean, low on punctuation, data serialization format with Python-style syntactically significant indentation - see:

In fact YAML is a superset of JSON, so Sublime Text could change the config files format to YAML without actually changing any of the config files themselves - maybe only changing // comments to #. :)
+1 and while we're at it, make quoting of object keys optional so the config parser wouldn't break on things like font_size: 12. That would be really nice.
Actually, the Douglas Crockford words that you quote are:
"Suppose you are using JSON to keep configuration files, which you would like to annotate. Go ahead and insert all the comments you like. Then pipe it through JSMin before handing it to your JSON parser." [emphasis added]
So indeed Douglas Crockford recommends using comments in JSON configuration files but removing them before feeding it to the JSON parser, which is exactly what Sublime Text seems to be doing.

Now, I know that just because Douglas Crockford says how to use comments in JSON, it doesn't necessarily mean we must do it, but from reading your comment one might conclude that he has said exactly the opposite thing, which he hasn't.

As for me, I found this thread when I noticed that Sublime Text removes comments from my user preferences every time I change the font size or color scheme via the user interface or key bindings (like hitting Control+Minus) which I found highly annoying, and looking for a solution I found this thread instead.

I find it surprising that anyone would not want comments in the config files - for those I can only recommend: pipe it through grep -v '^\s*//' and get over it.