Surely state regulations supersede local ones if there's a direct conflict, or they would if the city every complained and the matter were ever brought in front of a judge?
Local government doesn't give a damn; they're perfectly content to refuse permit issuance if you don't comply with their regulations.
In theory you're correct, but, courts aren't known for their speed.
EDIT: IANAL but I think the issue here is more complex, because the regulations don't "conflict", they create a situation where a bad outcome occurs only because both of them are in place.
Does anyone know if there are other "emergent phenomenon" effects in law and how they're handled?
The rules don't even conflict that way, there are legitimate ways to satisfy both requirements. All of them just have side effects that aren't desirable.
Thus there is no way to challenge the lower law as superseding as it doesn't technically. It instead supersedes most reasonable designs.
So long as the city is the one issuing the permit that allows you to build, then arguments about who the relevant authority is aren't really germane. The authority is whomever can grant you the permit, even if it puts you afoul of a different law.
