Well, of course. The service the waiter provides does not change just because you're getting a discount on the food. On the other hand, the service is also the same whether you order two expensive items or two cheap ones, so it shouldn't scale with menu price at all, but it does. Of course, using a percentage of the price does have the advantage of scaling with inflation... but then the percentage itself has increased significantly over the last couple decades, for no discernible reason.

Basically, nothing about tipping makes sense, so you just have to learn the thoroughly arbitrary rules.