I'm still surprised that Tom was just shipped off to another posting like it was no big deal. Even if he wasn't a transporter duplicate, the fact that he'd been stranded alone for eight years should have earned him some medical leave. Surely he can't be considered fit for duty!
Then there's the lab specimen aspect of his existence. You'd think transporter experts would want to study his accident, and medical doctors would want to examine him more closely - is he really a perfect duplicate?
And what about the paperwork side? Is he issued a new, separate birth certificate? What's Tom's date of birth, anyway? Is it the same as Will's, or is it the date of the accident? Is Tom entitled to half of Will's estate, whatever that may be?