I think it's because chihuahuas and great danes have all the same bits, just with different scales/shapes. Where as entirely new muscles take a lot more work to evolve.
And bone structure, just forget it. Mammals have mostly the same sets of bones attached the same way--a bat's wings are just gigantic hands with webbed fingers in skeletal terms.
I'd be very surprised if Chihuahuas and Great Danes literally have all the same bits. Canines are the most morphologically diverse animal, surpassing even humans. If there aren’t dog breeds that all have or lack a particular muscle, type of hair or bone I’ll be very surprised. Poodles have webbed feet for one, or just consider how some breeds have floppy and others pointed ears.
It’s reasonably likely the muscles that are universal among dogs existed among wolves at very low frequency and just exploded in frequency once they started hanging around humans. These kinds of hard sweeps happen when there’s either a very useful de novo mutation or a new environment makes a previously irrelevant or disadvantageous allele or trait beneficial. In humans think lactase persistence which was pretty much nonexistent 5,000 years ago or the Tibetan altitude adaptations which derive from the Denisovans who were living on the Tibetan plateau over a million years ago.
Floppy ears are just pointed ears that failed to rise - perhaps because they became too big. A German Shepherd pup has floppy ears and they eventually start to stick up, after going through a phase where they can't decide.
There is something impressive that a Chihuahua can instantly somehow recognise the Great Dane or Pekingese as of type dog, even at great distance upwind. Yet can react differently to cat, sheep, fox or squirrel at similar range.
Did a cursory search and it seems to be common wisdom that all dog breeds have the same number of bones and muscles.
While there are many differences between breeds and individual dogs, there are also common factors that link them together. For example, all breeds have an excellent sense of smell and hearing and have the same number of bones which are tied together by the same number of muscles, tendons and ligaments.
I’m sure 99% or more of muscles and bones are shared across the various dog breeds but humans have about as much genetic diversity as the average chimpanzee troupe and we have differences in our musculature. For dogs to be more uniform than humans given the speed and vigour of selection seems unlikely. Some breeds should lack vestigial muscles and others have them by more or less random chance.
Think about this: all mammals have the same number of neck vertebrae, 7, from giraffes to humans to mice, with the exception of (some)sloths and manatees.
That being said, dogs will have between 6 and 23 bones in their tails depending on length.
Artificial selection versus natural selection. New facial muscles emerging without design or intent is quite different from two separate groups of people trying to see how big/small they can breed a dog to be.
Selective breeding works incredibly fast on evolutionary timescales. You can get a selected population to no overlap with the parent population on your variable of interest in seven generations quite easily.
They examined four dead wolves. Four. Each had muscle fibers and a tendon at the appropriate place. Just not as pronounced. Where the wolves related? Apparently a pair was obtained from a taxidermist and a pair from Michigan. That is, this is hardly a representative sample of wolves.
Spinning a saga about dog evolution from examining 4 dead wolves is stretching...
2 facial muscles? What about Chihuahuas to Great Danes, is that not a more impressive evolution than 2 facial muscles?