See, as someone who studied neuroscience at Uni, I do agree with this. The two have merged, there is no denying it. But I would argue this. Wouldn't the V that is SoulKilled as soon as they jack into Mikoshi a more complete version of the two combined? Considering it didn't just copy V, it would have copied Johnny as well. Everything Johnny has experienced and gone through has been shared between the two.
I think out of the two, this is probably the better ending as V still has control. Johnny did something horrendous, he killed a lot of innocent people more than we ever could. Johnny doesn't exactly deserve a second chance, but you can find it within yourself to learn from them and not go down that route. Just like Johnny learned from V.
The two are basically the same it's just 'who's fronting'. Johnny is just back in the subconscious, rather than a full front personality fighting for dominance.
Johnny at the front however seems like he's happy but yet not. He sounds well, so sad. He's lost everyone, and he's alone again. The one person he clicked with is now gone. There is no positivity left for him. In the grand scheme of things, how long can Johnny live with what he's done?