(1) I'm not 100% sure what you mean with this question, but fuelcell.ssc defines the Simscape model for one block of the overall model. All of the Simscape blocks that are connected to the Solver Configuration block are analyzed together as a system of equations.
(2)-(3) Your equation looks like a forward Euler discretization of a differential equation. In general, I would say that you could consider using eta_a.der = (eta_a_new - eta_a_old)/dt and then you don't need to try and get old and new values everywhere, and you can just let Simscape discretize things. This would then work for both variable- and fixed-step solvers. If you really need to sample old values of variables, then you probably need an asynchronous sample-and-hold or an event that stores an old value. For your case, I would recommend just writing the equations as differential equations instead of as finite-difference equations.
(4) See Find Steady-State Operating Points for Simscape Models - MATLAB & Simulink (mathworks.com) for information on steady-state solutions.
