The thing about wood is it's very hard to cover up the grain. What makes Arisakaicon stocks so "plain" if you will is the lack of any grain in the wood. Now the color itself of the rifle is fine. Colors vary along the entire spectrum of light tan, through reddish shades to very dark, almost black. I have one of each although the very dark one is a Type 38, not a Type 99. What makes this one "odd" is the extreme grain. The wood is not what is typically used for these rifles. I do notice that the bolt is a late war bolt, plain handle and suspect that by this point they were using whatever wood they could get their hands on. I did run a quick search on Arisaka images on Bing which anyone can do and found two rifles with similar graining. One is significant because it is on the butt stock. Lower half is plain old no grain wood, upper half has the sharp crisp graining like on the fore end of your rifle.

Grain in wood can be emphasized by the direction and placement of the cuts. Some woods are more prominent than others but swirly grains are typical near and around branches, etc. So this is not a typical "cut" for an Arisaka stock but it doen't mean it's not an original stock. It probably is. The finish remains what is in question and I don't think it's possible to determine if it is original based on these few photos.

There is a strong possibility someone did notice the wood and worked to bring it out more than it had been. You should look at the overall condition of the wood, dings, scratches, sharpness of the edges, etc. Lack of dings or scratches and rounded edges are all signs of sanding. Is the metal recessed or is the wood still "large" and sticking out further. Are the barrel bands tight or loose?