Quick question. I have my cuttings rooted in clear water bottles and I can see lovely root growth on the sides of the bottles stretching to the bottom. I believe they are far too young to up pot them since they barely have any green. Will the light damage these roots that are exposed thru the sides of the bottle? 

It hasn't damaged these that have been exposed to light all summer.  

Not enough to make a difference

Plenty there to up-pot

I don't think indirect light would harm the roots. However, I'd avoid direct hit of sun rays.

As long as they have been acclimated to the light it should be fine. I would be more concerned about intense temperature than light, if the roots heat up too much that probably wouldn't be good especially if watering is inconsistent. If you are concerned you could always wrap or cover the bottles to filter out some of the light, but it sounds like they are growing well as is.

fignutty- your Maltese Beauty looks like it has some great roots and I like the idea of using the gallon container so you can see what is going on!

Light is not good for the roots but it won't necessarily kill them.  Most likely situation is that the plant will just invest into roots that aren't exposed to light.  There's no reason to allow that stress if you can prevent it, just pot 'em up black.  When I want to see the roots I pot in a clear container then put that in a black container so I can slip it out to see them when I need and have them in the dark otherwise.  Best of both worlds!

More on this topic here:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264407/