Alternate Dimension Exists
The only answer to all these questions is there an alternate dimension which can be accessed somehow (sci-fi fans will know better for sure) and Jin Woo managed to escape to that dimension.
To add to it, he managed to come back as most of the code base of the game was similar to the first version.
That can be the simplest plausible explanation I can give now. Which ultimately means Jin woo is alive. Since Jin Woo is alive, there’s a high chance he’ll come back.
As most of you anticipated Jin Woo and He-ju didn’t kiss in the final episode. We didn’t get the ending we deserved. We wanted more.
The disconnect between the two is most likely due to another season coming up in the near future.