I wait until they get their refund, just in case it gets stuck in processing/errors department or IRS makes changes to the original, you dont want your 1040X floating around in there not being able to get matched up with the original return.

What you don't want is the account frozen and the refund not issued because there is an amended return not yet processed.  That's why you wait for the refund.  

For an additional $6, i don’t think I’d bother…. I doubt IRS would generate a letter,  But would alert TP