You're right; the GPL can't directly affect those other works, which are "independent and separate works in themselves." All it can do is grant or deny you permission to copy, modify and distribute the original GPL'd work.
It can grant you permission with conditions attached. Copyright law does allow that. And unless you abide by those conditions, you don't have permission to distribute the original GPL'd work.
So I can release code under a licence which says "you can only use this if you send me a postcard," or "if you name you first-born son after me," or "if all software you ever write is released under the GPL," or "if I like your face."
It's my prerogative to grant or deny permission to use my own code as I see fit, under copyright law.
And I most certainly can release it under a licence which says that you may only redistribute it if you don't do so in combination with other software which is under a different licence. Copyright law most definitely does allow that, and that's what the GPL does.
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