Etymonline itself says "figurative sense is from 1835".
There's a few things to note here. Firstly, in 19th Century Britain, geology was the gentleman's science par excellence; The Geological Society of London rivalled the Royal Society in respect and membership. It was not unheard of for fossil collecting to be done in top hat and tails (okay, that was just one particularly eccentric fellow, but still). Mary Anning had supported her family by selling sea shells on the sea shore.
As such, anyone who wanted to take pride in being intellectually current, wanted to consider himself reasonably knowledgeable on, and to hold informed opinions about, geology. We could compare it to the buzz around web technologies of the 1990s dot-com era.
As such, it's not at all surprising to find a geological term used figuratively, any more than it was to see nightclub posters telling us when and where they would be @ in the 90s.
The other thing is that embed is a simple word of obvious construction. It would be unusual to see someone use a geological term like quaquaversal used in other contexts (though Thomas Pynchon once used it of a beard), but we can see em- + bed and immediately widen it mentally to the figurative use. A figurative use that arguably is really no longer figurative (do you think of geology when you hear it?).
So, on we go through the centuries, or about century and a half, and the Apollo mission is making use of a computer guidance system to hopefully steer people to and from the moon. What to call this configuration?
Integral. Very bad choice, the "integrated circuits" used in it were still a hot new technology in themselves. They already had a meaning for integral and its variants.
Intristic. Invites the question, "As opposed to what?". What we could call the extrinsic parts of a Saturn V that's in space, are those parts in a control room in Texas.
Bound. Maybe. Maybe a bit too wide though.
Inherent, ingrained, nested. All of these make me wonder "what isn't?" given the context.
On the other hand, one novel feature of this computer, was that the integrated circuits, and the wiring between them was physically covered in epoxy in a way that would bring embedded to the mind of anyone looking for the mot juste to describe it physically, since the end of the 1800s.
So, of course they could have called it something else, any naming decision could have gone differently, but that embedded was chosen is pretty reasonable and understandable.