I'm not sure how the transparency argument is relative. You seem to be confusing energy, which depends on the frequency of individual photons with intensity, which is the number of photons. Shine all the low-energy photons you want, and you're just going to add heat, not create photo-products or ionize.
These are more than just bond rotations (with only slim exceptions, bond rotations have the same energy state) from photostimulation. You can flip cis/trans bonds (main mechanism of retinal), ring closing in vit D, and cause all kinds of increased free radical activity [1]. In particular, blue light interacting with certain chemophores, such as catechins, are relatively prone to photoactivation [2].
Ever seen polycarbonate that's been around blue LED light sources (not sunlight) for a very long time? It yellows. That's not "just adding heat", that's chemical bonds breaking.
Transparent just means the entirety of the body can be bathed in light.
EDIT> cis/trans retinal -- should have remembered that