I have brought this issue up before a while back, but my edits were reverted in regards to it. For the Affiliations parameter in infoboxes, we have a convention on this wiki to assign factions to characters who were only allied to those factions and not members of them. As a result, we have it listed that Connor was affiliated with the Templars from 1777 to 1778, Arno was also affiliated with the Templars, Élise de la Serre with the Assassins, and so on and so forth. I understand that it can be argued that to be allied with a faction one is not a member of can be considered an affiliation, but I would argue that for the sake of clarity, the Affiliation parameter should be reserved only for membership. The core reason is pragmatic: it would simply be confusing for some readers, even if they understood the plot, and we hint at our meaning by clarifying dates.
For example, there have been at least one case in Star Wars where the Jedi Obi-Wan Kenobi had to work briefly with the Sith Lord Darth Tyranus also known as Dooku. During the Second Galactic Civil War the Jedi even allied with the Empire. Now if Wookieepedia had, in light of the former situation, put Sith Order and Confederacy of Independent Systems for Obi-Wan's affiliations, would it not be confusing for readers as to what is meant? I know a Star Wars example might not be the best since it's a much larger franchise, and it's a different wiki, but the point is that labeling an affiliation for a character because that character was allied with that faction at one point, no matter how brief, can be extremely confusing for the audience. In some situations, you might have a character who is forced into helping another character who is normally an enemy to survive. I don't remember off the top of my head if there has been such a scenario in Assassin's Creed yet, but my point is that I think our logic around this is unhelpful to readers and certainly confused even me several times.
Affiliations should be reserved only for actual membership. It's confusing to label an Assassin a Templar at one point because the Assassins happened to enter into a truce or alliance with the Templars. That would be like listing Soviet Union or even Communist Party of the Soviet Union as an affiliation for FDR because the USA was allied with the USSR in WW2.