Are you sure that the intent is to obfuscate? There's no other possibility? Maybe shrinking the size of the file transferred to increase performance?
Think of it like modding. Customizing something to fit what the user wants is an incredibly powerful thing and can actually increase the usage of your web app. Think of greasemonkey plugin, which allows you to add some pretty cool functions to certain sites that don't already come with that site. Just because you can't imagine the possibilities doesn't mean someone else won't.
Fine. I'll buy that. But that's a "functionality" thing, not really a "proprietary vs open" thing. Your average user doesn't know or care about that stuff. All they care about is whether or not the website works the way its supposed to.
Fear is the greatest salesman. -- Robert Klein