I think what is going on is they are talking about the evolution of the penguin BEFORE the DNA samples were ‘alive’. If you push back their ages then you compress the evolution that got them to that state.
For example, if they had a penguins from 1,000, 10,000 and 100,000 years ago and compared them to the modern penguins you would find an increasing amount of difference as you go further and further back in time.
Based upon their analysis they claim that most estimates of date of common ancestry based on DNA comparison between two extant species WITHOUT a good fossil reference were underestimated.
If the time needed to derive the measured amount of divergence between a panda and a raccoon for example, is pushed back twice as far, that means that the rate of evolutionary change is half as fast as previously expected.