My usual grammatical spidey-sense has let me down here.
The sentence "I can’t begin to fathom how their tiny bodies would cope with what they had to carry" FEELS complex to me. I feel that
i) "how their tiny bodies would cope" is a subordinate/dependent clause.
ii) it also feels like the object of the main clause "I can't begin to fathom".
So I'm currently labelling it like this: Main clause [I can’t begin to fathom] + subordinate clause [how their tiny bodies would cope] + prepositional phrase [with what they had to carry].
Is this correct as you understand it - I feel there's some grammatical info I've missed here for this confusion to occur!