I'm not being able to accompany the discussion, so apologize if these arguments have already been talked over. Kindly ignore them if it's the case.
But please consider the following:
(1) Cython, as a single entity, will be unable to run the library all by himself. He will necessarily have to hire staff, so he will necessarily integrate another one of the options into his own. Even if his standards of hiring are incredibly high and demanding (which is something dwarves would approve of, mind you). But really, picking Cython means that there will also be an adjutant staff of humans/halflings/dwarves or whatever else, unlike with the We that are able to do everything on their own.
So Cython also has more of an integrating value.
(2) There is talking that Cython will see the library as "part of his hoard", and that in a distant future he might just pick up and leave, taking the library with him because "well, it's mine, so I'm taking it". However:
-This will still be a library in a fortified Karak. And Karak vaults many times outlive their citizens. If we are talking about Cython leaving in an unknown future, there is also an argument that he would simply lock the library and keep his stuff there, since using abandoned Karaks as vaults is quite the dragon thing to do.
-The We consider knowledge they acquire as "part of themselves". So if the We also decide to move, there is no logical reason as to why they also wouldn't want to take the books with them. If the We grows and develops, the books will be parts of their brains, knowledge and self, so they would be even less willing to leave them behind in a supposed "migrate elsewhere" scenario that many are attributing to Cython as well.
"But if the We were to leave, we could just copy the books before they go!"
Well, that argument also applies to Cython.
And that argument is flawed in the sense that some of the books in the library are the kinds of books we won't really want to see copied.
And finally. The We are still young as a hive mind, from what I understand, and they need to read the books in order to know their content and "assimilate" it. Much of the attraction of the We is that the We might be a librarian that "knows where everything is, everywhere, all the time". So that necessarily means that the We will have to read all the books in the library to function effectively.
All of them.
That might feel attractive to some, but I am disinclined to have a growing hive mind be obligated to read things that would give even Mathilde pause. Cython, on the other hand, is perfectly suited for that sort of weight.
And really. With Cython, the "absolutely restricted" section would literally have the books in his own presence. No better safety than that.