well, i can't figure out how the ending is supposed to work, because it doesn't make sense logically... so, the nanites rewrite the DNA in V's body so it in effect becomes johnny's, and if V decided to stay in her body (or her engram i guess) her/johnny's body would reject her engram, how, isn't it just a digital recreation of her mind/memories/personality etc, how's that supposed to clash with the body's DNA?
as for the true ending, i think it's coming in dlc, something along the lines of... step 1, find means to extend v's life, step 2, find way to reprogram nanites, step 3, find unaltered source of V's original dna to use as blueprint for nanite rewriting. final step reprogram nantes.