I think Miranda will end up at 1B, not because of his inability to play 3B, but because I think it's more likely that Kirilloff will either remain unhealthy or won't develop as hoped. Not saying he will, I just think the odds that he ends up developing into a cornerstone player are lower than the odds of Julien, Lewis and Lee at the moment.
And if Julien, Lewis and Lee force the issue, I don't think the Twins will be inclined to give Kirilloff a long leash. Fair or not, there's just other prospects that are just as talented if not more.