it is an issue with the light produced. led diodes are a planar light source (look at the planar radiation pattern) that give off relatively more collimated rays which is unnatural compared to the sun and filament/hid sources that has more divergent rays. it's like listening to music through a cone shaped speaker driver vs. the actual waveform produced by an instrument. diverging vs converging echos etc.
the brain perceive objects illuminated by led's to be distant in space compared to HIDs and filament sources. same as how the brightly lit building a mile away is perceived to be distant despite it being brighter then the room you are in due to ray angle eccentricity. so light from leds don't stimulate accommodation at the eye as much (the more divergent the more stimulation, hence minus concave lenses) which leads to accommodative lead related eye strain. in other words, led light is actually too 'comfortable' for folks that have issues with accommodative insufficiency. the general population tends to have an issue with accommodative lag/excess hence they have no issues. there's a reason why optometry testing machines you rest your head on and look into still use filament sources.
we use computer monitors for eye testing in the optometric clinic and we noticed weird changes in our results when we changed from old dell CCFLs to newer led backlit monitors. eye movement was decreased and accommodative amplitude changed and the results were repeated when we A/Bed it.
flicker and spectrum is a red herring. filament bulb flicker too and your own blinking is low hertz flicker. daylight has tons of short wavelength content.
I think very soon the industry will pick up on this because folks in optometry and neuroscience already know about this. there is an indoor olympic track and field training center in china that downgraded their expensive LED setup to sulphur plasma. something about the brain the 'sensing the ground as being more present' which is pretty wacky but not really wacky since we already have tons of literature about how LRV of flooring affects gait.
personally I switched out my expensive optisolis leds in my home for cheapo CFL spirals and 12000k philip 'snow white' tubes and if anything the ambiance is superior. maybe that's why the corner store doesn't feel as chill since they swapped the overhead tubes for leds