Final answer:
The free energy diagram with the 'Reaction coordinate' axis illustrates the reaction's activation energy and transition state, whereas the diagram with the 'Reaction progress' axis shows the change in Gibbs free energy relative to the reaction quotient (Q). Activation energy is not depicted in the latter because it is a kinetic factor, while Gibbs free energy is a thermodynamic state function.
Step-by-step explanation:
Your understanding of free energy diagrams is essentially on the right track. The diagram with the x-axis labeled 'Reaction coordinate' indeed represents the energy changes during the course of a specific chemical reaction. This diagram is useful for visualizing the transition state, the relative energies of reactants and products, and the activation energy (Ea) required to reach the transition state from the reactants.
On the other hand, the diagram with the x-axis labeled 'Reaction progress' relates to changes in Gibbs free energy as a function of reaction progress or reaction quotient (Q).
Activation energy is not depicted here because this diagram is focused on the thermodynamics of the reaction—namely, the change in Gibbs free energy—which is a state function and is independent of the path taken, including the activation energy barrier overcome during the reaction.
Activation energy is pertinent to the kinetics of the reaction, whereas Gibbs free energy changes are pertinent to the thermodynamics and the equilibrium position of the reaction. Both diagrams provide different, but complementary, information about a chemical reaction.