Is the primary question whether or not the attack is magical for purposes of whether or not it goes against mundane resistances? I think that the ususal Common Wisdom is that it depends on what the primary ability is, not what augments. In any case, there's that clause about resisting magic with mundane abilities, so in any case, it seems likely that dodge would apply.
Some might argue that, since blowing people up is a suitable thing for a thunderstone to do, that this means that it's not outside of it's primary area of impact, and, as such, the mundane ability ratings should not apply.
OTOH, I could argue that the magic only causes an explosion to occur, and it's that then naturally occuring explosion that hurts the targets. Meaning that the mundane resistance would apply. From that POV, you could roll the thunderstone's ability against a 14 first to see if it goes off, and then apply an attack based on the resultant explosion. But that's probably a little far to go. :-)
Mike
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