Hey bigolebuds!
On the specific pic you shared the root ball is quite nice already. Probably time to transplant to bigger pot.
Truly it is not good for the roots to get exposed to light, although you are not the first to use transparent cups. They will be just fine if it is temporary phase, and you move them to final pot after noticing the root development.
If you want to help it a bit, you may cover them with aluminium foil and only expose to light when inspecting the roots.
My very first grow was an auto all the way till the end in transparent 8l water bottle. It survived and provided me with some nice results. But for sure it did not help her to thrive.
Enjoy the grow!