Gibbs free energy=potential free energy? (Transition state theory)
Yes both mean exactly the same thing.

By definition gibbs free energy is the total amount of non pv work that can be extracted from the system. Non Pressure-Volume work refers to the work which does not allow change in both volume and pressure of the system. An example of non pv work is electrical work which is done by cells and batteries in creating a potential difference about its ends. 

Now pv work is related to kinetic energy of the molecules of the system. We can see this by two ways. First is that pressure and volume both are dependent on movement of molecules. Hence increasing pressure at constant volume is the same thing as increasing kinetic energy of the gas due to which there are more collisions of higher magnitude. Similarly increase in volume at constant pressure also means increase in kinetic energy of system. Second is that pressure and volume are both related and dependent on Temperature by gas equation where temperature of a system is directly related to kinetic energy of the gaseous system.

So whenever pv work is done by or on system changes take place only in kinetic energy of the molecules of system and not in the potential energy of system.

Hence whenever non pv work is done by or on system, changes in only potential energy of the system takes place. So Gibbs free energy is same as potential energy of system.