What's the difference, though, between custom HTML/CSS and custom JS in terms of licencing? All of them could be developed in-house and have the same "proprietary" licencing (i.e. can't be copied and used on other sites) - after all it's illegal to clone someone's site and host it elsewhere without permission surely?
I think the FSF have got this one wrong - if there was a way to make JS closed source, then they might have a point, but claiming JS can be "proprietary" just because it's minified or developed in-house (and not usable on other sites - after all, a lot of money could have been spent developing - or purchasing - the JS) is barking up the wrong tree. As long as the JS works cross-platform on the major browsers, I see no issue myself.