The difference is that nobody forces you to comply to standards. If you want to hack around on your device, install third party software, concoct your own APIs and drivers or patch the kernel, nobody can stop you (and shouldn't be allowed to, either). While you can argue that a restrictive system is a sort of standard as well, you are forced to comply to that standard with no alternative, and that's bad.

Besides, standards, at least open ones, are usually collaborative efforts of multiple actively involved parties, while restricted systems are controlled by a single entity - which again is bad.