How about thinner and softer vegtan? I just got vegtan goat hide from Tandy which is quite thin and soft. It's discontinued so the price was good.
I used to work part time as a sushi chef and used small towel to wrap around my knives when took them to work. If the knives are not kept in sheaths (mine are kept in wood covers), tip of the knives can pierce into the flap of the roll case. I also have a roll case from Global and have that problem with yanaki knife. For cleaning issue, I always clean all knives well (and sharp) after work before put them back into the case. So I never have to clean the case.