I was doing a little research on the etymology of John recently. (I suspect that Riordan's "Jackson" is a reference to John, where "Jack" is a form of John, and Percy Jackson is likely meant to be "Perseus Son-of-the-Grace-of-God", which is a reflection both of his parentage and his deliverance as an infant cast out to sea.)
The Online Etymological Dictionary states:
masc. proper name, Middle English Jon, Jan (mid-12c.), from Old French Jan, Jean, Jehan (Modern French Jean), from Medieval Latin Johannes, an alteration of Late Latin Joannes, from Greek Ioannes, from Hebrew Yohanan (longer form y'hohanan), said to mean literally "Jehovah has favored" or "Jah is gracious," from hanan "he was gracious."
Greek conformed the Hebrew ending to its own customs. The -h- in English was inserted in imitation of the Medieval Latin form. Old English had the Biblical name as Iohannes. As the name of John the Baptist and John the Evangelist, it was one of the most frequent Christian given names, and in England by early 14c. it rivaled William in popularity and was used generically (in Middle English especially of priests) and as an appellative (as in John Barleycorn, John Bull, John Q. Public).
The Online Etymological Dictionary
My feeling is that all 4 Johns you mention are very positive and admirable characters. Usklass was certainly graced, as a foundling who rose to become a supreme King. Likewise, Strange, Segundus, and Childermass are all fairly graced.
John Barleycorn is worth looking at, as he is a very famous figure in English paganism.
Regarding "Segundus", it means "second" in Latin, thus "John the Second". I'm not sure how to interpret that in context, but there does seem to be some history regarding Latinate English names. This is an area of interest, although I know very little about it. (Offhand, I recall Stoppard's "Septimus Hodge" from the play Arcadia, which is worth seeing/reading, particularly if you are a Strange&Norrell fan.)
Regarding Jonathan vs. John. The names may be distinct but the root is the same and the meanings are similar: "God has graced" vs. "God has given".