Orwn, I would still think it more likely that, in the context of all the diminutives in the verses, Carroll was thinking of the 'little atomies' pulling Queen Mab's carriage in Romeo and Juliet ('
atomy is a diminutive
fairy creature or
sprite of surprising smallness') and used 'Dear Atom' as a the shortened singular of this with which the diminutive Manikin could address his equally diminutive wife.