I guess it depends on where you live. It's not common to routinely put bleach in home wells in our area. We get our well water tested for various things every few years and have never had a problem with it. It must just depend on where you live and the terrain, plus the type of soil, groundwater and well structures you have. I didn't realize that in some areas, homeowners bleach their wells annually.
Bleach is a toxic substance. That's why it works as a disinfectant. Too little is ineffective and too much can kill you. Or the chickens. That's the reason people are talking about proper dosing being an issue. Pesticides are the same way. They can kill you, your chickens or your pets, if you use too much.
I've never worried about the quality of puddles, but I don't have any right next to the run, where it could have more contamination by manure. If you have some low spots right where the run is draining, maybe think about adding a little soil there, to bring the level up to the surrounding ground. It probably wouldn't take much and then you wouldn't have to worry about it anymore. You might only need a bucket of dirt and a hand trowel to add a bit of dirt. If it's a larger area, a shovel and a garden rake can help. Over the years, I've done a little re-contouring in the yard here and there, to help with the spring run-off and puddles, from melting snow.
In general, I'm more protective of what I expose young chicks to and less protective for healthy adult chickens with healthy immune systems. When you free range, they get exposed to a lot.