if i were writing the ending i'd do away with the whole dna mismatch engram rejection, as there's no logic to it... instead:
the nanites have completely rewrote the neural pathways in V's brain, meaning that if you placed V's engram into their body, they'd be forced to think like johnny. V would still believe and have whatever ideals and convictions (if any) as they did before soulkiller, so V is still V, but the decisions that they'd make to achieve their goals and live up to their ideals would resemble johnny's handy work. so, v is in command but johnny follows orders in the manner he chooses (or V does rather as there is no johnny) to, more or less. stay with me here, it's a bit rough.
now, this plays out one of 3 ways, and based on your relationship with johnny...
ending 1) V ignores johnny throughout the game, cuts him off, doesn't let him speak, ends conversations as early as possible, etc. minimal johnny contact. V trys to remain him/herself, but is unable to separate their thoughts from johnny's, because s/he lacks the knowledge that would give them an idea how johnny thoughts work, how he operates, etc. and through repetition V slowly turns into johnny, having their mind forced through his thought process relentlessly. eventually v becomes a mean spirited, manipulative, angry, violent killing machine, very much resembling johnny in actions and deeds, but V in overall intent/ideals.
ending 2) V lets johnny vent, at least hears him out, but the relationship is combative and antagonistic on both sides. V does more than the base johnny content, gets to know him and his friends/associates, and has a decent understanding of johnny, how he works, his personality, etc. (a view not just derived from silverhand himself, but tempered by those who knew him)
through persistence, determination, and most importantly knowledge - V is able to separate their thoughts from johnny's and force themselves to think how they would normally, and through repetition V slowly forces their neural pathways to something more closely resembling V's thought processes. however, because their arguments overall reinforced the will of both parties, they believe their respective manners are correct, they both dig their heals in, and it's more difficult to push those pathways. so, V remains mostly V, however there is almost a flip side that carries a stark contrast. not exactly D.I.D., or bi-polor disorders, but it's there and it's noticeable.
ending 3) like ending 2, V listens to johnny, they have a few arguments, however overall, especially when johnny starts to open up... their relationship becomes fairly cordial, even friendly. V starts to have an influence on him (like when rogue actually mentions you're a good influence on him, and he's a fairly decent human being now, and not such an A-hole). both V and johnny drop their guard bit by bit, and more of you rubs off on johnny then him on you. he stats to mirror your thought more than you do his. through this shift in his personality his thought process change little by little and by the time of the soulkiller bit his thought processes are somewhat in between V's and his at this juncture already. the result is that the neural pathways are less fortified, and are already closer to V's original process, and it's easier to push the goalposts. as a result this winds up with the V engram being most like the original V.
---edit several times) the allure of the go into the net ending is that supposedly V's engram will stay as unaltered as possible in this state, and at some point you may actually get a new body or something. and V stays V, while johnny gets the body.
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