From the paper's abstract (emphasis mine): "Wavelength influences multiple aspects of visual performance, yet its role in spatial resolution remains incompletely understood due to confounding factors such as luminance differences, chromatic aberration, and intraocular scatter."

They then did some modeling to estimate how well the results could be explained by scattering, chromatic aberration and, neural sampling (the cone cell density factor that you mentioned). They concluded that none of them could completely explain the observed results, but their results seemed to suggest the bulk of the effect is due to optical effects, with neurological factors as a secondary cause.

Refining existing knowledge by examining phenomena in more detail is how science should be done. The pressure to focus on discovering entirely new things is a major cause of the replication crisis.