You are touching on one of sciences many secrets: there is human guesswork and subjective judgment used.
The basic concept of comparative morphology is you look at the creature’s body and compare it to others to see which other species it is most alike.
Clearly, the ability to do any analysis is very limited for extinct animals, because in most cases we only have skeletons.
The wide degree of variation among modern dogs with fairly recent common ancestor might fool people analyzing their bones into thinking they are different.
One key difference here is that dogs are artificially selected. So the genetic variability has been tested out through selective breeding. This would not happen without involvement of humans.
When looking at a fossil, it is reasonable to assume it is a wild animal, that it is “average” for its species, that the species is pretty uniform, and that humans were not breeding the animal.
In summary, we can trust comparative morphology for ancient, extinct animals because we can safely assume they bred naturally.
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