What gets me is him being a Captain

Why though? I know he doesn't make captain until after Sigma Octanus, but Keyes' rank's not really relevant to who he is as a character, it's an incidental detail. Surely what's important is that the character - i.e. personality, mannerisms, etc - is consistent. Would he be any different as a character had he already been a captain going into Sigma Octanus?

I need not explain Miranda's situation

You kinda do. While the article names her Dr Miranda Keyes, but it describes her as "a brilliant UNSC Commander who is dedicated to understanding the technology, language and culture of the Covenant" so I don't see where canon is broken in any way, she's a UNSC Commander in keeping with the lore. The doctorate seems to just be a way of fleshing her out and making her character more than just 'Captain Keyes: the Girl'. Furthermore, it is justifiable in existing canon. She joined the UNSC military academy at 16 (second youngest person to do so, ever) and her mam was already on her second doctorate by that age, surely it's reasonable to say that she could have been a child prodigy in the same vein as her mother. Could that not also be an acceptable way for the show will include the J Keyes/Halsey relationship without having someone turn to camera and say "See them two? They fucked"; a bit of 'show' rather than 'tell'.

The Human raised by the Covenant is definitely canon breaking, unless this is some kind of Starkiller situation.

It's certainly justafiable in universe through the Jackals, as has been mentioned elsewhere. Either it's like 'The Cole Protocol' where it's part of some convoluted scheme by a Prophet, perhaps to raise sleeper agents/infiltrators. Or, it's the Jackals just being mercurial and mercenary (they've already been established as privateers for the Covenant) and just not giving much of a shit about the greater philosophy of the Covenant, like they've been shown to be in the Kilo 5 books.