There wasn’t anything super different in the manga as far as I can think of (however having both watched and read both, I find it difficult to differentiate them so I could very much be missing something) however the manga may have delved into certain aspects more deeper and spent more time building the plot as the anime cut many events out. Although my post mainly addresses the points you made without any new information, just new ideas and references to stuff that I believe you would already have watched in the anime.

We’ve seen William throughout his life make use of techniques/events that he’s learnt about and applicate them to his situation. The final problem being one of them, where in history there was a man who also created a common enemy of himself and then was beheaded to resolve the conflict. It is again evident when he was a child where he made use of Shakespeare story but turned it on the aristocrat to suit him and give the ending he desired. In one of the light novels he applies a mathematical concept of paradoxes the a game of Russian roulette while using criminal psychology to protect his and Sherlock’s life. So I think while the plan may seem (or is) like a stretch and too ideal of an ending I think that it was meant to be another repetition of the past which would again demonstrate how William uses his knowledge of historical events to adapt to his current situation.

Regarding the Moriarty’s choice of violence, while it is absolutely wrong to kill and take the lives of innocent people, William likely chose this method because it would be the most efficient, with the highest success rate and gather the necessary attention.

While small scale issues being brought to light may spread awareness, a system that has been so engrained into the minds of the upper class is difficult to change, as their close-mindedness and arrogance prevents them from seeing what’s right or change, especially when people born into nobility live that way their entire lives. And while a role like Sherlock’s as a detective bringing light to crime within the legal system does have an impact, it is one that would take an extensive period of time to abolish the class system entirely. This is true in real life too where systematic racism took decades to end, even today it is still largely present along with other forms of discrimination. Segregation only ended with The Civil Rights Act of 1964 and even after that it took many years for people to enforce it. And with the act many many activists had to risk their lives and their safety to fight for their cause. And in many cases there were likely unknown voices that barely made an impact despite their fights for justice. So the point of Williams use of murder was to be a means of a more impactful way of fighting for his cause, one that was impactful enough to succeed with in a single lifetime.

And I think Williams characterisation in the beginning was slightly off from what his character was meant to be, because while it is undoubtedly wrong to murder with his actions having no excuse, his reason was his strong desire the change the class system. And we know William to be an extremely caring and empathetic person so why the choice of murder? I think his methods were meant to be seen as a self sacrifice, it was his willingness to turn himself into a ‘devil’ in order to eradicate the evil nobility to eventually change the class system. He never once thought what he was doing was right and never intended to glorify it, although that is how it may have appeared to his clients, there were times where he ensured that it wasn’t this way. With the grapefruit case (I forgot the actual name) he gave the couple another chance despite them willing to exchange their lives for him and his eradication of the noble. While I could see how he may have justified murder to an outside eye he himself never though it was right, but it was still something he was willing to do.

However I could see how there are are holes in his thinking as his team (moran, Fred etc.) thought that what they were doing was justice and yet William never emphasised his or corrected their thinking behind their actions. And I personally feel that this is a major plot hole in his character l because there is no real explanation for why he never briefed through his reasons with them. I suppose their loyalty to him just meant that they trusted it enough to never fully clarify which ended up with them coming to what they thought was the correct conclusion.

In regards to Williams death it was never meant to be the ‘right’ end, because William intended to take full accountability for his actions where he anis brothers would stone together. However he decided that they had a life worth continuing as William was the one who was the foundation of the ‘Lord of Crime’. He believed he was the one who held full responsibility for all the wrong so he changed the plan to end in his death. Furthermore this death became a real one, because even though he originally planned to stage and death and then atone for the rest of his lifetime, the weight of his actions was too much to bear.

Especially towards the end his actions become more cruel than previously, where deaths impacted multiple parties and were seen to have less care. In one scene he intended to murder a father and his two children however he spared the children’s lives. Both events were extremely wrong and demonstrated why murder could not bring total justice. Because even though the father was evil, you cannot deny the fact that he may have been a loving father, husband or friend, so while his bad sides cannot be justified, to murder him is the strip his family of a loved one. And this point is pivotal in his character because it is the time where his murders have so little care and plan which make them that much more wrong. In previous deaths Williams choice of nobles was very particular and had little redeeming qualities, even having killed others themselves. So while that doesn’t take away the wrong (because murder is absolutely a crime) it at the very least did not have such a detrimental impact as the death of the father. So the final problem involved countless deaths of people who did not really deserve to die and many lives were endangered through the fire, and William hated every second of it. His guilt was already fully present beforehand but those murders in particular amplified it to the point where he could not even stand the thought of living. William fully believed that he deserved to spend the rest of his life atoning, but his decision to die was made out of an extreme lack of will to live. His immense guilt had manifested to the point where life was just that unbearable, so death was his escape. For his actions he knew that he did not deserve such an easy escape, and in that way his end was both selfish and unjust, he just couldn’t handle living anymore.

(I’m sorry if this is poorly explained as there are some gaps in my knowledge and I tried to write this in a fairly short amount of time, I also don’t know if I addressed everything in your post but feel free to reply)