Congratulations on your upcoming trio!!! The xray is great, very definitely 3 puppies in there.
I'm no vet and certainly can't read an xray as they can, but I do agree that the pups do
look very long/big ....and then they come out so little.
I've had xrays done each time I've had a pregnant female and each time though I did not see the vet measure, they've always let me know whether or not they thought the pups would pass through the birth canal with any foreseeable problems.
Many 5 lb dogs whelp pups with no problems, just as any bigger dog might need a c-section. It just depends on the build of the female, the size of dogs/pups in the lines of your bitch/stud, etc. If all your vet said to you was "she's small so she might need a c-section", I would call them back and ask specifically that they look at them again and let you know what they thought about the skull/birth canal comparison.
Good luck to you!