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Does this kit come with 2 lower hulls?
You must be thinking about the Tamiya style of M48 hull... In Dragon kit the return rollers are attached to the upper hull part and fenders are separate. And yes, this kit comes with two complete upper hulls and with two complete engine decks.
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the later 2 version through redesigned rear doors. Same rear deck that was used on later (Magach 3/M48A3 and after) diesel powered versions.
That actually is not true. M48A2/Magach 2 used similar, but still significantly different and not interchangeable with M48A3 engine decks and rear doors. The kit comes with correct newly tooled parts for M48A2.