I did read the whole thread but can't see how folks think it is OK to have cracks in the metal of the gear case. These cracks are not just cosmetic, as I can dig a fingernail into them enough to tell they go into the metal a ways. Like many here, I've been working on engines and machines my whole life and can't say I have ever seen a crack in a vital part that didn't result from problems, or cause problems. Either the metal is too thin, or cheap, or poorly alloyed or stresses exceeded specs. And I know for a fact that stresses have not approached specs.
I'm not doubting that some people ride on gear cases that have spider cracks for many happy thousands of miles. I'm only saying that while my bike is under warranty and with only 3,500 miles I am not comfortable accepting a structural defect in a vital part. Now if I had to pay for it out of pocket, like the OP would have had to do, then I get the argument to leave it alone.
At this point I'm just curious how common this problem might be.