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.
If blue light actually impaired vision, that would be very notable. It would mean that removing the blue 'channel' for an RGB image would improve acuity. This is not what the study showed, however.
It is mainly just the basic fewer cones bit you mentioned. Which, btw, is easily experienced if you ever look from a distance at neon or led signs that only emit blue light. They'll persistently look out of focus when compared to their surroundings.
It is extremely noticeable for me at night because I can never fully focus on signs using blue LEDs, while red LEDs give me no problem.