I think the one thing people who answer this have been dodging (and you actually stumbled upon with one of your examples) is that of the specifically named characters I know (not including all the protagonists of GTA, since each one has their own story and some of them are not likeable by any stretch of the imagination.) I can say that Homer is usually not malicious (as a major character in a series that has been running for 30 years, I am sure Homer has done something actively malicious... but by and large and in the best loved era of the season, the problems he causes others are not malicious in nature and more caused by profuse stupidity and inability to grasp subtle clues.).
And despite Homer's flaws, most of Homer's vices on this list are used for comedy and are more out of him being motivated by simpler desires. To whit, Homer almost always understands he did something out of line when there is an emotional outburst directed at him than he does when the displeasure is subtly voiced, and he goes on to try and make amends (Homer being an idiot that he is, normally does so in a way that shows he still doesn't get the core concept but is trying.). In addition, despite all his flaws, Homer is absolutely devoted family man who treasures his wife. On the few times Homer is put in situations where there could be another woman, the conflict of the story is him trying to avoid the implication that he would cheat on Marge with this person. One of the all time best Simpson's Episodes "And Maggie Makes Three" is framed as Marge and Homer telling Bart and Lisa the reason why there are no pictures of Maggie in the family photo albums. The entire story is Homer being an exception jerk to Marge during her pregnancy with Maggie (again, given the period of time in the show's history it was to a degree that was almost out of character), but the point of the story was that, by the time the audience learns where Maggie's pictures are, it fully redeems Homer and is one of the most emotionally satisfying conclusions. And while both Bart and Lisa have little respect for Homer, it's made clear that Homer's ignorance of their interests and hobbies, it does not mean Homer has no interest in his children. Often, he just doesn't know and is trying his best to learn what it is that his kids enjoy. In many cases where Homer isn't the direct cause of the conflict, he will straight up tell his kids he doesn't know why they are upset, but he does know his job is to be there for them when they are (This is more common in Hommer/Lisa or Homer/Marge stories as Homer and Bart tend to be less at each other's throats (at least in the metaphorical sense. In the literal sense it's a running gag) and Marge/Bart tend to be more out of touch with one another. Homer/Maggie rarely happens given Maggie is still an infant, but it's strongly implied that Maggie thinks the world of Homer and loves him unconditionally, warts and all.).
When Homer with the exception to the alcohol issue, any commonalities of Homer with actions on the list are typically not successful when he tries to do them with intent (to the point that they come back to bite him in comically karmatic ways) or unintended results of what he believes are helpful actions combined with his ineptitude.
In a more general way, adding some kind of sympathetic reason for why a person is a jerk can go a long way. Note that when doing this, it is an explanation, not an excuse. The expectation is that by the story's conclusion, the underlying issues will be resolved, and any "jerk" behavior is done more as an in joke with the former victims than it is with malice as presented.
In this case, consider Ebenezer Scrooge from "A Christmas Carol" In the events upon joining the book, Scrooge is a very unpleasant person and takes personal delight in knowing that people do not enjoy his company and makes his disdain for Christmas very well known. But it's clear from almost the moment that the plot kicks off, that with every Ghost that visits, Scrooge is clearly recalling that much of his attitude not only caused him further pain, but it doesn't instill fear he thought it did. His own nephew (who tried and failed to involve Scrooge in his happiness) makes a joke at Scrooge's expense at the party Scrooge would have been at had he not declined the invitation). And when Scrooge does profess amazement for Tiny Tim's humility and love for life, it's quickly dashed when Bob Cratchit proposes a toast to Scrooge's health as it was his employment of Bob that made the dinner possible, only to be interrupted by Mrs. Cratchit, who points out that the Christmas Feast is as good as it is (and by all account's Bob is clearly grateful for what small amount of food they have for the dinner) in spite of Scrooge and that he's a terrible boss. But she retracts her complaints when Tiny Tim, who does not know Scrooge admonish his mother with the famous line "God Bless Us, Everyone." Although unspoken, Tim's words simplify the point he makes: Scrooge may be a terrible human being, but he is still one of God's children, and thus isn't deserving of his Mother's Wrath during a Toast at Christmas Diner.
Scrooge again praises the wisdom of the child but is told by the Ghost of Christmas Present that while it's not his place to know the future, but he doesn't like the direction where it's heading without some change... Tiny Tim will die. And when Scrooge is contemplating this thought, the Ghost hits Scrooge with a decisive blow and what's so powerful about the spirit's words is that the Ghost isn't teaching Scrooge a lesson: He's quoting Scrooge at what is possibly the most despicable line he gives when we first meet him:
If they/he are going to die, then they had better do it and decrease the surplus population.
Scrooge had unknowingly condemned Tiny Tim with his words because Tim was poor... and was met by Tiny Tim defending Scrooge because Scrooge was a human.
It's here where Scrooge's personality has the most noticable shift. Following this incident, Scrooge meets the Ghost of Christmas Yet to Come, who never says a word to Scrooge. Scrooge has a one sided conversation but it's clear that all the questions he's asking the Ghost are questions he already knows the answer to but is too scared to say outloud.
In the conclusion, Scrooge is fully committed to changing and makes amends with everyone he wronged at the start of the story without a trace of hiding deception. But when he comes to the Cratchit house, he takes a tone that Bob is familiar with and presents himself as a cold uncaring boss for the build up until he reveals the reason for his visit to give Bob a raise and to give Bob the feast he deserves. Whatever the reason for the joke, its clear that Scrooge may still be a stern boss and can put up a serious face... but within the distant future of the book, Scrooge gained a reputation for keeping Christmas better than anyone.
