I'm not a native Polish speaker, but my native language is Slovak and it's very similar. In Slovak you can say both "Z akej planéty si?" and "Z akej si planéty?" and both sound natural. Starting a sentence with "si" (jesteś in Polish) doesn't sound very natural, although it does a bit more in yes-no questions. You can always add subject (i.e. "you") to the beginning of the sentence, like "Ty si z akej planéty?"
You're right. And both forms are correct in proper context. That said, for some reason when asking about places, e.g. From which city, country, planet are you? We use "Jaki" not który. I've never really thought about it, and man, it's weird. It seems to me that "który" is more about differentation from group of the same objects.
The second one puts pressure on the "z jakiej planety". [ With rising intonation ] It's a form that could be used in repeated question asking for clarification [ as the answer was surprising perhaps ]
It's same as in Spanish, you can change the word order to emphasize the verb or the object [although in Polish there's more freedom ]