I'll do my best to answer.
I own four SE guitars. Two from Cor-Tek Surbaya, one from Cor-Tek China, and one from World Music Korea. So, IMO the quality control is universally great. Its at the point where if I can about blindly trust that sig on the headstock; I know I'll be getting a quality instrument. While chance kinda dictates lemons are to be expected, I have yet to come across an SE I didn't like. That said, a couple things to keep in mind if and when you buy: SE guitars are checked at least twice. Once at the overseas factory, and again at the factory in Maryland. They also make a very long journey through a multitude of climates and temperature shifts, so issues will pop up from time to time. Case in point, my 35th ani had a lifted fret. It seems these are pretty isolated things among SE owners, at least here. With the SE line, you are about guaranteed to get a great instrument that is fun to play and well made, and no... Paul did not pay me for that plug....at least not in conventional money (Nutella will make me say anything).
PLEK....nah. While I like the idea of the PLEK job, don't see much reason to PLEK an SE. I don't think they need it honestly. I did do spot leveling on all of mine, but that's more like me being anal and fine tuning the setup. I did'nt have to do it. On the Paul's Guitar SE I bought last year, it was already setup with 4/64" action, no buzzing period, straight from the factory. After my leveling adjustments, its down to 3/64". That's it. So, I wouldn't see a PLEK job making any more drastic of an improvement there.
On the S2...yes, they are worth it and I've never heard a peep about shoddy QC on them. Its hard to choose between SE and S2 given the option, in many ways the S2 is basically what an American made SE would be like. I honestly can't choose between them, though IMO, based on the ones I've seen and played, SE's look aesthetically superior.