He is still the commander when resting right? So he logs the lot. The factored timing for augment crews is only used for FTL reasons. The can squeeze greater than just 100hrs per 28 days or greater than 900hrs per year out of you. They do however count all of the time towards upgrade requirements, pay etc.
The OMA states that all time in Ek is considered hard time. There is no mention of early parole though.
The don.