if your Li-ion battery is 2kWh, and your lead acid is 1kWh, then your deep cycle capacities are closer to 1.6kWh (80% DoD) and .6kWh (50% DoD). in effect, the li-ion battery is around 3x larger, if you are treating them nicely.
losing efficiency - what do you plan on doing?
strictly from a power conversion standpoint, you will lose some energy in a switching power supply vs using it at 48v or 12v, but I don't see that as being a serious concern.
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