I've looked into much of what they're discussing in the article you linked. What's occurring in an EMP, and Solarflare is that both create an 'induced force', or 'induced voltage'; you need three things to create a moving current; a magnetic field, a conductor, and relative motion. All of these things are relative to each other; meaning, a Faraday cage is a 'nice thought', but the Joules, or amps that the Sun can create can, and probably will simply melt all Faraday cages given a strong enough flare. Even an EMP could have similar effects based off of proximity to said blast; in this case, rather than the worst case scenario, it could simply be the 'cage' isn't up to par for the momentary magnitude of force induced.
Not saying it won't help, or possibly work, I just would never bet the bank on it.

A magnetic pole reversal is an entirely different critter all together, All electric generators, and motors are built orientated to the current polarity of the present field; retrofitting to a new field orientation is, or will be on par with a flare; stuff just won't work; 'caged' or not.

Do you have any further information, or are familiar with what I've stated; perhaps they do take all of this into account?