Mostly what I am seeing is less "Flood is bad" and more "Flood is poorly timed" which for the Ascians amounts to the same thing, but it's useful to at least have some sort of clarification on it. I imagine as a whole the Floods are what they want, but it needs to be set up properly ahead of time. Make the cracks, then let the Flood happen. Ardbert and co just did their jobs too well.
Was it mentioned how exactly these cracks were made? Were they just events leading up to it that allowed it? So for Bahamut's, things like what became the Burn would be starting signs of the Seventh crack, while for the attempted eighth it'd be...Shinryu/Omega due to timing, I guess? Or is this all stuff that happens behind the scenes and not noticeable until the aether starts to change.
Edit: I realize that the cracking could have been the Battle at Silvertear Falls for the Seventh Calamity. Probably fits better in the timeline, but still hard to say.