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This is a good objection. The system might be so complicated that people don't understand how to correctly express their preferences.

Definitely a challenge for many mechanism design approaches to intervening in the world. As I understand, the only really solution is to experiment in the real world, see what holds and see what doesn't, and tweak accordingly (e.g. test out different interfaces that communicate how the mechanism works!)

Rationality expectation is good if irrationality of others does not harm rational voter.

In this case, a well-organized and mathematically adept voter can and will harm less rational ones, thus skewing the balance instead of restoring it.

No. Irrational voter harms himself. Rational voter just gets what he wanted.

That's too close to calling them lesser beings for my comfort. They harm themselves, so who cares? Greed is good!