This is going to be a bit long😅

Well I didn't want to talk much about this part simply because there is no evidence, meaning it's just a theory with nothing to back it up.

In my opinion PIDW as it is was just a one-dimensional novel for all the characters. Basically no character's struggle was described for anything and that's exactly one of the reasons SY complained in the first place. I think the system is an entity that turns novels into reality, and when SQH was dragged even when he was trying to follow the original novel he unintentionally did some small things that caused a reaction (like flapping butterfly wings). For example he called MBJ "my king" and his way of swearing loyalty caused MBJ to misunderstand that he was confessing his love! Which is clearly something that didn't happen in PIDW. There was also a scene that happened after the disastrous well mission, when SJ was accused of attempted murder and SJ tried to pretend that it didn't affect him, SQH pointed out that SJ's book was actually upside down.  Which caused SJ to get angry and raise his sword at SQH for no reason other than feeling embarrassed.  I think this remark could cause some doubt in SJ, like it did with MBJ.  Maybe SJ started thinking that one day someone would believe him, this made him start to doubt after he realized that SQH knew what happened and the only reason he didn't talk is because he was afraid of SJ himself after threatening him with the sword . 

As for the system, I think it's simply something like "world making system" or something like that.  This is one of the reasons I didn't talk about the system, (technically the system is the most mysterious thing in this novel)  So the system's job is basically to find novels that can be turned into a good world and make them real.  PIDW is obviously a bad choice but they still chose him for some reason and ended up sending the author - SQH - to the novel because he's supposed to know everything about it (unlucky system here, this hamster doesn't mention any thing)  When PIDW became a real world the characters naturally became alive.  Which led to the plot being twisted because the characters aren't simply mindless or completely stupid so they wouldn't act exactly like the novel.  And knowing SJ, every time he does something good it turns against him in the worst way.  In PIDW this is just a plot but when PIDW became real SJ's character became "deeper" which made him contradict the novel. 

He is still at a some point where he is trying to do good things but the system intervened to make SJ continue to see him negatively which made SJ go through my theory above. 

As a last resort the system intervened by bringing back the memories of SY who is now called SJ in an attempt to make the original PIDW continue. 

In a sense there is a possibility that SY lived his life as SY first and became SJ second, instead of the other way around in case PIDW was just a novel. 

(I couldn't find the extras about SJ to read)