Energy conservation is... tricky. Under Noether's Theorem it's guaranteed by time translation symmetry, which is kind of sketchy at cosmological scale. My understanding is that it can be violated under conditions of changing gravitational fields or somesuch, but don't really understand what specific circumstances do the trick.

Ed: don't get hung up on "expansion of space is fuelled by light" or whatever, they only picked a photon for their thought experiment because it was easy to reason about.

The total “energy” of all photons in the universe is declining, but the acceleration is increasing. Hard to believe the first is causing the second.