Would this work for an E3? That is the threat I take more seriously. The E1 might or might not happen but CMEs are pretty common. With them it's not if but when. We have had close calls recently so its only a matter of time before we get nailed by another big one like the Carrington event.The containers would make a decent lightning protector. For solar storms the best thing you can do is isolate your home from the grid - pull all the main breakers.
For an HEMP type EMP event a shipping container is not very good and grounding a shielded area is just adding antennas to bring in more of an E1 pulse. Steel is not a good barrier for E1 pulses- the resistance is too high. You need at least aluminum and better yet is copper and the best is silver. Multiple layers of shielding with multiple layers of insulation is much better than one layer of any kind. You almost never want to ground a shield for an E1 pulse, it is best left isolated because the high voltage/amperage is travelling through the air and ground to a depth of over 12 feet.