I don't think it was ever said that the Intrepid
class was the fastest in Starfleet. All we learned was how fast she was, not that others wouldn't be faster.
(FWIW, the ship that did get called the fastest in Starfleet was the Prometheus
from "Message in a Bottle". Warp 9.9 was the highest speed the ship did in the episode, and since the VOY hero ship can demonstrably do better than that, it follows that we never learned the exact top speed of the Prometheus
Also, even if it takes the VOY hero ship 70 years to do 70,000 ly, it doesn't necessarily follow that it would take 7 years to do 7,000, let alone 0.7 years to do 700. The shorter the trip, the higher the speed that can be maintained, apparently... After all, the E-D was supposed to cover about 7,000 ly in less than three years in "Q Who?". Or then the E-D was twice as fast as the Voyager
, which is a very real possibility. That is, as regards "on paper" top speeds, which are the ones being discussed in both cases. I practice, we have seen both ships run into major problems around warp 9.7.