I'm not certain, but...
It sounds like the writer is attempting to be very poetic in describing a living creature that is just a bare remnant (shadow) of who they once were and is extremely thin (dressed with bones).
If my understanding is correct, the two examples you gave can be grammatically correct, but each is at differing levels of poetic language.
"...just that it was a shadow that was dressed with bones."
This is clearer and more in the pattern of modern language.
"...just that it was a shadow that with bones was dressed."
This flipping of the verb/adjective following the noun is less commonly used today'
To see the second example more clearly, you can look at it with full punctuation:
"It was a shadow that, with bones, was dressed."
I hope this is helpful.