A couple of things:
Reentry-capable second-stage/ship enables:
Mars aero breaking (don't know if they plan on this)
Earth return aero breaking (this would be a very obvious one)
And most importantly, use of a common design for both the crew ship and the fuel-haulers, as the latter has to be reused...a lot.
So pull the crew compartment, insert propellant tanks, use as tanker to deliver to LEO. Leave crew compartment, use for ship.
The bulk of the vehicle would be identical in both cases, saving development money.
This is pretty much the least-capital intensive way--you only have to build lots of two fully reusable parts.
Same reason why it's a common engine as well--the upper stage uses 3 non-vacuum raptors, and 6 vacuum raptors (IIRC), while the first stage uses 42 non-vacuum raptors.
Effectively, their design is to minimize the development time/cost at the expense of a reduction in "efficiency" which can be made up for in quantity. Since literally -all- prior ideas/attempts/programs didn't happen because of cost to start, rather than efficiency in the long run...this is a smart way to do it.
So it's the same strategy they already use for Falcon...one engine type at a time with only a nozzle change for vacuum ops, one vehicle diameter, etc.