I’d argue that this could be a deviation in how Harmonic Convergence was animated between the 2 fights (since there is an obvious depiction change between them), especially since Korras case was the only time we saw the planet and how it was being effected by harmonic convergence, whereas with Wan we only saw the spirit world.
And, narratively speaking, it really doesn’t make sense to think this is Vaatus feat. The energy enveloping the planet was coming directly from the co-joined spirit portals.
We even see this energy around the planet fade away right as HC ends and the spirit portals separate after Korra and Raava re-fuse.
Besides, Vaatu in the 2nd HC was still sealed within the Tree of Time, and he explicitly needed the spirit energy given off by the combined spirit portals in order to break Wans seal. Why would Vaatu, in a moment where he needs to absorb amplified spirit energy, expend more of it?