--> Why hide the book?? No-one would know that my keynote refers to it, so it can sit on my shelf with the rest

Sure, but you still need to keep it safe with no guarantees you could ever find a replacement.
--> Perhaps, but it seems to me that the chances of Github being shutdown are pretty low...
Low, but not zero. It is completely centralized and owned and operated by Microsoft, who could simply decide to discontinue their support for it at any time.
--> The additional passphrase is something I've only just learned about, this seems like it would help me feel more secure, so I'll look into it.
Here you go:
https://github.com/bitcoin/bips/blob/master/bip-0039.mediawiki#from-mnemonic-to-seedhttps://wiki.trezor.io/PassphraseI still feel uncomfortable just keeping the 12 words written down on paper and hidden, so I'm going to use my Book / my Github repo as a 'key' or 'cypher' for the time being... No worries if others find it 'unnecessarily complicated'

It's not just unnecessarily complicated, but also drastically increase your risk of loss.
You can mitigate your chances of losing access to the particular version of the book by choosing a book that will likely continue being published, like the bible.
The Bible is probably one of the worst possible choices, actually. There are
literally hundreds of different versions, with each version having dozens of editions, and even the same edition of the same version being different due to having multiple publishers and/or printers. Even something as simply as line spacing being slightly different or page size being slightly different and your page/line/word schematic is rendered completely useless and your coins completely inaccessible.