SHorties are basically just the collector and then a flange. LT are the collector from each of the 4 cyl on each side and then they continue back to a new H or X pipe depending on the design, then either High Flow cats or no cats.
As for the warrenty issues. The law is there but you will never win unless you have really deep pockets. I have been through this quite a few times so trust me. Dealers make more $ when you pay for a repair then if it is covered. With that said if they see an aftermarket part on the car they will usually do whatever they can to say that part increased the HP and original design of the car creating different conditions therefore whatever the failure is, it is not covered.
Now we call know that a 3" exhaust will not cause an alternator to go, but since they know you need a new one and they can pull this kind of stupid explaination, YOU now have to take them to court over an alternator. It is never worth it and yes you lose every time.
Unless your entire engine blows and it is a large expense item it is never worth it and dealers know this. So you will pay to play. If you mod with non warrentied parts expect to never have a drivetrain repair covered again. Some dealers are mod friendly but that is reallllllly rare. If you are going to mod you have to be willing to pay for it.