The inner liner is not fully attached to the outer fabric, so when the top folds towards the inside, the liner is prone to folding more than the outer fabric. I wouldn't worry about extra folds in the liner. If the main roof had extra folds it probably would not stow properly.
Anything that moves will wear, the question is how long will it last. Probably the biggest problem is where the stowed top rubs against the boot cowl. The pressure from this can be adjusted a very small amount, every little bit helps IMO.
