Hey there! Sorry for the late reply, but to provide an answer for your question (I apologize in advance for the wall of text):
Essentially yes, Cloud's speed rating comes from keeping up with Sephiroth who in turn is much faster than Zack who could keep up with Bahamut Fury.
While it may sound tricky on the surface, there are some things to consider for the speed rating:
We don't consider Travel Speed as necesserily completely separate from reaction and perception speed, especially given some verses and authors, such as DC and Marvel do
openly establish them as separate. However, the character in question when moving around still has to take notice of their surroundings and avoid obstacles. In Bahamut Fury's case, it didn't only flew through space, a the beginning from the sequence you
can see it coming out of the Asteroid Belt, meaning it has to properly avoid crashing into the asteroids, for which it had to perceive them and avoid them. Now, while it's true that the distance between asteroids in the Asteroid Belt is around 966,000 Km (or 600,000 miles) Bahamut Fury covers around 450,000,000 km of distance per second, that would mean crashing into around 466 asteroids every second if he couldn't properly maneuver during flight. There's the additional case of the already mentioned Exaflare, in which he launches himself into the orbit and once he reaches the appropiate distance from the Moon he stops his momentum right away to face it and prepare the attack.
This leads into another point: while Bahamut Fury is indeed mostly static during the fight (though it
does move a couple of times), Zack is still
reacting to all of its attacks, one notable being the
Hexafang move which Zack can
easily outru and is the same attack Bahamut Fury
uses to prepare the Exaflare, shooting the spikes at the Moon which reach it in about 2 seconds. Nothing really indicates that Bahamut Fury's attacks should not scale in speed to his movement, reactions and perceptions as explained above, and Zack can keep up with all of them without bigger issue. Then, later on, Zack is shown to be completely overwhelmed by Sephiroth in the Nibelheim Reactor during their fight, who in turn became much stronger after falling to the Lifestream, then after becoming Safer Sephiroth and then again upon his resurrection in Advent Children who is the incarnation Cloud held a fight with and defeated with Omnislash V5/V6.
A doubt that might come up is "Why doesn't then Bahamut Fury blitz Zack if it's so fast?" and the answer is because it can't, Zack is fast enough to keep up and catch up with it without problems. Another possible thing that may come up is "Bahamut Fury's attacks are much slower than light in the battle" but you have to consider what was mentioned above, the speed seen is how Zack, the character that is fighting and we control, is pereceiving the events and movements and for him the attacks move at a much more reasonable pace, which ties into the pace of the gameplay itself that follows him and is given to the player. I think a good example of this would be Vincent's fights with Weiss the Immaculate in Dirge of Cerberus: in
the first round, which you are supposed to lose, Weiss completely surpasses Vincent in every way and this is displayed by Weiss being able to defeat you in a few hits, but also by flash stepping and moving around so fast it's impossible to keep track of him much less aim and shoot him. For
the second round, when Vincent has been empowered by Omega, the gap between him and Weiss has been narrowed and Weiss can be beaten and the boss fight proper reflects this, and how much stronger Vincent became, by not only being able to damage Weiss and be capable of withstanding his attacks much better, his flash steps are gone and now he simply slides around the battlefield at a much slower pace, representing how Vincent can see and follow his movements (there's even a small yellowish tint in the background to emphazise both fighters are moving at super speeds).
