Does Migration Assistant move Mailbox (mail.app) IMAP data?

Recently I used migration assistant to move a user from a Lion machine to a Mavericks machine. I couldn't get it to work via direct ethernet (famous "1 minute remaining" bug) [1] so I migrated from a Time Capsule backup.
After migration the User's mailbox was initially empty, though the smart folder and standard folder configuration was as expected (Gmail IMAP setup).
Overnight the Mailbox refilled -- but Activity Windows suggested it was pulling data from Google, not from a local store.
It's as though Migration Assistant excluded the IMAP data [2], expecting it to be reloaded from source. (In this case it might have worked, but risky for several reasons). One expert I know says this is in fact how MA is supposed to work -- but neither of us could find ANY documentation.
Does anyone know if this is correct? Even better -- have you seen any documentation?
Thanks!
john
[1] In retrospect the source machine was configured for automatic logout and it's possible that the logout attempts confounded MA.
[2] Time Machine's standard exclusion plist suggests IMAP data IS backed up.

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