Yes, the base is stained, mostly from just being in the same pot for many years I would guess. I do not wash it or try to remove the staining. I should try to place it in something more tractional.
I tend to like exposed root as you will see in some of my other trees. Root over rock is one of my fav styles. This tree has been raised once and much of the bottom was under dirt for unknow number of years. This could also be the cause of the coloring.
Since I am in the north where 5-6 months are frozen outside, my indoor plants suffer from very dry conditions. The house gets lower than 25% humidity. Moisture does not stay on the surface of anything for very long.
I will give it a try, see if the color can be removed or lightened. Though a good outdoor stint will tend to bleach it some.
Yeah I also struggle when forced to bring my outdoor trees and plants inside. Terrariums work well, but often too small for bonsai trees, and take up a ton of space. Using a spongey moss soil mix also helps maintain moisture levels and humidies the nearby air, necessary for health. Only problem with organic soils is the roots will not develop correctly for bonsai.
Always learning from my own mistakes. Good luck.