Borges was all about this weird mix of the mystic and the banal. If you haven't read The Library of Babel, it is brilliant.
I see it as, on its face, referencing the idea that Judas was asked by Jesus to turn him over to the Romans, and so wasn't actually a betrayer. There is a Gospel of Judas, one of the Gnostic Gospels, that has been interpreted this way (but this particular translation is disputed). Others have made various arguments over the years as to what this whole story really means. So Runeberg's works are various explanations for why that might have been so. His first book argues that Judas betrayed Jesus to be a kind of mirror of the holiness of Jesus's sacrifice. In his second book, Runeberg instead suggests that Judas did what he did as a way of renouncing all hope of closeness to God, a sort of ultimate humility.
But I think there's more going on (and there always is with Borges). It's interesting to me that Runeberg changes his mind in response to criticism, but it's not clear whether he's actually convinced or cowed. There's also an interesting irony in how the story ends. Borges starts by putting Runeberg in the same camp as various early Gnostics, who were seen by what became the Christian church as heretical. Gnosticism's tenets could vary, but usually there was the idea of finding secret knowledge of the nature of the universe (and the belief that our world was an imperfect one, created by their version of the devil (the Demiurge), to imprison mankind). So on the one hand, Borges says that Runeberg would've been relegated to obscurity with the other Gnostics, but then at the end, suggests that Runeberg was outcast and ultimately died because he found secret knowledge that was too much for him. But it's also unclear which of his two theses are actually the one that was right, and the whole thing may be a coincidence or lunacy.
Layers upon layers.