This is quite common and pretty harmless. The scratches you see don't go very deep, nor are they very wide. My All-Clad saute pan is nearing 10 years old and has a ton of micro-scratches on the interior. It still performs beautifully.
That said, the scratches can grab onto proteins and cause sticking. However, this is simple to prevent with both oil and proper pan preheating.
When a pan is preheated properly the metal expands, essentially closing all of the micro-scratches. This prevents the proteins from grabbing onto them and getting stuck. You obviously need oil/fat to assist with this as well.
To properly heat a pan to the appropriate temperature I suggest using the water drop method. If you put a cold pan on heat and drip a drop of water onto it, the water will sit there for several seconds then boil away. As the pan gets warmer this will happen more quickly, fizzling away in a second or so. Once the scratches start to close something weird happens.
First, the drop of water will break into a few mini drops which scoot around the pan as they evaporate. This is a sign that you are almost there. When the drop of water stays whole (mostly) and scoots around the pan like a mercury ball, this is the perfect temperature. I the water instantly vaporizes on contact, you've gone way too far and need to let the pan cool down. At this point you should add your oil/fat, swirl it around, and immediately add your food. (Make sure the mercury ball of water is gone before adding oil).
Also note that the mercury-ball phase is definitely too hot for unclarified butter, and may be too hot for some extra-virgin olive oils. They may instantly smoke upon adding.
Again, it's important to have your oil and ingredients in place (mise en place) before you start. It's quite easy to skyrocket past the mercury-ball phase if you have to open your oil, pour, and then season your ingredients.
Boiling water leads to evaporation, which leads to concentration of anything dissolved in the water (and there will, unless your water is distilled, always be something dissolved in it); that concentration can lead the water to be supersaturated and for trace minerals to precipitate out of solution. If you are getting water from your municipal mains, chances are it's perfectly safe either way.
The appearance of 'muddiness,' however, seems very weird to me. Water can't become muddy on its own; by 'muddy' do you mean 'cloudy'?
Best Answer
In my mind, bread baking containers are divided into two categories:
1- Pans for shape
Many bread pans are used only to give bread shape. These can very from "normal" loaf pans for sandwich bread to baguette pans.
These pans need to just stay out of the way of the heat as much as possible. Baguette pans are even perforated for this reason. They are usually made out of very thin steel and don't need to be expensive at all.
2- Pots for heat and steam
Artisan style bread needs high initial temperatures to produce steam that opens up the bread and builds the crispy crust. It also needs to have a steamy oven during that initial crust-forming period. Consumer ovens don't usually retain heat very well and are not built with steam injectors either.
Putting the bread in a pot helps with both issues. By preheating the pot, the bread will be exposed to a large, pre-charged, thermal mass right at the beginning of baking. Then as steam escapes the loaf it will be held close to the bread and give you a crispy crust.
Pots to do this need to be able to hold a lot of heat so cast iron or ceramic vessels are used. A stainless steel pot with a lid probably wouldn't do very well because it wouldn't hold much heat and would shield the bread from the high heat.
Since you mentioned no-knead bread, I would think that you are planning to make artisan style bread rather than soft, sandwich bread. If that is true then I don't think a stainless steel pot would be the best choice. Use either cast iron with a lid, or forgo the pot idea and bake the bread on a pizza stone and spray some water in your oven for steam.