You're more correct than you realize. Frogs aren't reptiles. The DNA mismatch would be even worse.
They are just taking in account the concept that important coding sequences might have been conserved.
What is more unlikely was how the DNA information was able to be preserved. Without a buffer it would have denatured long ago.
Hell, this is why bananas are fruits even though they don't contain seeds. Modern-day bananas have been selectively breed and spliced to create what we think of today as a banana. They don't have seeds because they're hybrids and are sterile. Same goes for most other seedless fruits. They're seedless because of genetic engineering by making hybrid plants.
No these cases is more due to the fact that they were cultivated for their lack of seeds. Bananas are seedless for example because they are triploid and propagated by people who didn't like seeds . But you can make genetic hybrids all the time in the lab both animals and plants that incorporate genes from other organisms and are still capable of sexual reproduction.