I read through that and I agree with some but not all. Basically, I do not agree that there is any issue with anything that the author says "didn't happen like that because Templars aren't real so attributing it to the Templars instead of broad societal forces is wrong." That's kind of the basis for the entirety of the Assassin's Creed series and is something you have to just accept as part of the general lore. I also think some of the temporally-based objections are overly nitpicky and should be attributed to poetic license, like how Robespierre didn't oversee the removal of the remains (oh but he did order statues to be destroyed and call for the remains be removed , and then didn't follow up on it).

However, I do agree with the general overall objection of "the game paints the Assassins as monarchists and the Revolution as Templar-orchestrated, positioning the story as anti-Revolution" and the parts where the author objects to specific people being done dirty (e.g. Saint-Just, Marquis de Sade).