It was two years ago now, but I certainly had no problems as an independent tourist. I was told beforehand that Sakhalinsk is no longer a restricted city and did not require a permit. I didn't have one and was fine.

You can travel in an our of Yuzhno as you please. I visited the two closest cities and some of the wilderness and then made my way by land to Okha (Oxa). I needed my passport to buy the train ticket but that's been the case with all long-distance Russian trains I've been on. No problems buying my domestic flight, nor getting in/out of the country in the first place.

I take the situation in reverse of any official guidelines...as it's Far East Russia officials tend to be more relaxed and lenient.

Any specific info, feel free to send me a PM.