Hobby Search shows the original list prices and images of the parts and instructions for both kits. The super parts are an additional sprue, and the parts are added on top of the base kit. You can even see that the instructions for the super version show what non-super parts are not used, such as the vertical tail fins. The super kit has all the parts needed to build the non-super version.
VF-11B Thunderbolt - List Price 3,080 Yen
VF-11B Super Thunderbolt `Macross PLUS` - List Price 3,740 Yen
It might be worth shopping around some more to see if you can find the standard kit cheaper, since it should be, but it could be an issue of availability.