That's all true and fair but I think the original question was why are they even allowed to be present in the Astartes when the Emperor himself decreed that no Legion should maintain a Librarius department. So far we've got the options that the Emperor changed his mind sometime before he placed himself on the Golden Throne and allowed Librarians to continue to serve. That Gulliman and the other authors of the codex: Astartes decided that legion vs. chapter was a lovely wording loophole and put them in place or that they just plain ignored the Emperor.
Personally I think that the former is the most likely as I can't see the loyalist primarchs responsible for the codex ignoring the emperors literal commands and I've not convinced that a Primarch would play word games in the same way as the church did with the "no men under arms" given that the command came direct from the big E.
That said, was Guilliman at Nikaea? I don't think he was, in which case he could legitimately claim never to have heard the dictat and so ignore it when writing the codex possibly?