I am signed up for about 5 rental car companies programs and find they are all about the same overall. Once you have qualified for the super-duper program (i.e. Emerald Club via National) things change a bit more. Most have a counter bypass system.
I suggest you look at some of the other rentals. I just changed from Hertz to Thrifty - kept the same class of vehicle, same period, and saved almost $300. The biggest change was in base week price. Then came the $50/day versus Hertz's $67. YMMV One thing that surprised me was changing locations where the vehicle is picked up had a big impact on the cost as well.
Always shop around for travel costs - you're bound to find a better rate out there.