One of the common settings in which the "mysterious ways" defense is raised is in attacks on the existence of god based on the existence of evil. In such attacks, it is suggested that the existence of evil is inconsistent with the characteristics of god. But this only holds if the evil is gratuitous or unjustified. Thus, whether god's ways are mysterious does indeed matter for this argument. Additionally, in stories like Job, the mysterious ways may be asserted as a way of undermining mankind's authority to make moral pronouncements. If human kind can't justify their moral stance, god's justification of his acts is unnecessary. Again, mysterious ways matter.
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