Since you are using volume measurements, it is hard to say if your dough formulation is responsible for the results you have been achieving. For example, if you are using flour and water measured out textbook style, your hydration would be around 80%. That would be extremely difficult to work with, whether by hand kneading or using a machine. Most people tend to be off more on the flour than the water when these are measured out by volume, so I suspect that you had to add a fair amount of bench flour to get the hydration down to where you could work with the dough.
The ingredients and quantities you mentioned don't throw off any red flags that I can see. On the assumption that you used more flour than you stated or, alternatively, less water than you stated, the yeast quantity and salt quantity both appear to be in range. The methods you used to knead the dough and to allow it to ferment both at room temperature and in the refrigerator should not have limited the crust coloration. Normally, the IDY is added directly to the flour, without hydrating in water. But, if the water you used was warm and you hydrated the IDY in it anyway, that shouldn't have affected the results. If you did hydrate the IDY in warm water, did you add the salt to the water at the same time by any chance?
If you used bread flour, you should have been able to get decent crust browning without having to use oil or sugar. As between the two, usually one uses sugar to promote crust browning. If you want to take a stab at using some sugar, adding about 2 1/2 teaspoons of sugar to your recipe may be a good place to start. At that level, you shouldn't get premature or excessive bottom crust browning when baking the pizza on your baking stone.
Very frequently, a very light colored crust is a sign of overfermentation, where there is insufficient residual sugar in the dough at the time of baking to promote good color development. However, unless your dough was several days old when you used it, you should have gotten decent color. Using excessive amounts of yeast, particularly when used with very warm water, can also cause the dough to ferment too fast such that the residual sugars are low by the time you use the dough. I can't tell you whether your yeast levels were too high without knowing more precisely how much flour you used. However, if the amount of flour you used was actually greater than you stated, for the reason mentioned above, then I think your yeast level was not excessive.
By any chance, did you put the pizza in a pan of any sort and then place the pan on your preheated stone? If you used just the stone, at what level was it placed in your oven?
Unless there is something that you have not told us, or unless it is a problem with your oven as vitus has postulated, I am stumped. Maybe next time you can take some photos if possible so that we can see if there are any other clues to help us solve your problems.