The romance of the MC and ML can be said to be built on misunderstandings. Although, that is not entirely the case. The ML appears to have fallen for the MC quite early on, but the MC only really decided to accept the ML quite late, somewhere around chapter 80 or so? At that point the MC proved his decision to stay with the ML through some... really painful s*xy time...I winced inwardly at that part.
It was quite touching to see the ML's dedication towards the MC. (Dude hugged a corpse to sleep for 5 years wtf.) The earlier parts (before the system forced the MC to push the ML into the abyss) was this mutual happy daily life arc. Both parties were content with life as teacher and student. At this point, ML was a really devoted student and his fondness might not have crossed into love yet. Either that or he just hadn't realised his feelings yet.
Then came the 'I'm back from the abyss!' arc. It kind of threw the MC of guard since the ML came back faster than expected. But oh well, he went with it and tried to awkwardly avoid the ML as much as possible thinking that his student hated him for kicking him into the abyss. (As per the original story) The two kind of fell out because of this, so when MC was being framed for some crime ML failed to defend him, resulting in the MC being thrown into jail. After escaping with some help, the MC travels to a city and has a dream along the way. In the dream, he abruptly realises the cause for the strange the point gaining method thus far. This part was honestly gold. The rationalisation that the MC used to figure it out plus the ever so helpful kiss from the ML had me rolling on the ground in laughter for a good while.
Then MC fakes his death, leaving our little puppy devastated. Of course he returns after 5 years, but many thins have changed by then. This final arc helps to fill up some plot holes, introduce us to a deadpan father who says ridiculous things and give our side characters a little spotlight. The ending is a happy one despite all the hardships our MC and ML had to face. The troll system continues to troll, but at least it was kinda helpful towards the end. We are also treated to some extras including an interview where 'interesting' questions are asked about the MC and ML's relationship, as well as a an occasion where the original ML (the one from the harem stallion novel) and the puppy love ML are swapped. No, original ML didn't kill MC on the spot, but it was so damn funny how the MC realised that the ML was a different one. (Really? Your technique in bed is too good to be him?)
Come to think of it, a lot of the misunderstandings stemmed from the MC's initial over reliance on the original story's plot. Because of that, he kept misreading the ML, causing much suffering on both their parts. The MC also realises this near the end, thinking that if only he understood how the ML actually felt all this time, they could have avoided so much pain and suffering.