Hi TorontoJoe,
In the old way, if you stick a cutting in the ground, when do the roots get light ? ... Never . They seem to grow down to the opposite direction of the light.
It is unusual for roots to need light. They need to stay in the darkness.
Sunlight could even burn/cook the roots on a sunny day. So this is something you want to avoid.
One way to avoid root damage from light is to keep the roots inside the dirt (add surrounding dirt). The other is to use a solid dark cup, and insert the cup you have in the solid one.

Interesting - I get that strong sunlight can do damage but would never have guessed that indirect light in a north facing window would be a problem in these clear cups. I'm noticing some of the lower roots turn a bit brownish -I wonder now if that's why

I've grown large fig plants in plastic water jugs that admit some light to the roots with very good results. Roots don't need to be in total darkness. This was inside my greenhouse.

The plastic cup and your window glass will filter out nearly all the UV-B light. Greenhouse poly does the same.

The thing I'd never do is put that cup in standing water. That's my definition of over watering.

The other thing I won't do is take the plant out at that stage to add soil to the bottom. You'd ruin those roots. The light won't hurt the roots. I've grown cuttings in clear cups with good results. And covering the roots with soil would just be temporary. New roots would soon be on the outside and you be doing it over again.