"The EPA now must perform a risk assessment that is among the first steps in setting new limits under the Toxic Substances Control Act."

What's stopping them from coming back with the same or higher acceptable levels of that's where the evidence leads?

That’s not an accurate summary of the ruling. The ruling orders the EPA to re-evaluate the safety of fluoridation, but does so because the statutory evidentiary standard here is preponderance, not overwhelming evidence.

(It’s also not a ruling “against” the EPA. It’s entirely consistent with the statute, and the EPA will presumably act in accordance with it and produce yet another study demonstrating marginal-to-zero harm associated with fluoridation below 1.5mg/L.)