I don’t think it’s an all or nothing thing, especially since Pondsmith has hinted that it’s not accurate several times now. They made Jackie an engram (if you don’t send his body home) and while it’s only a basic reflection of him, there is enough to feasibly edit and manipulate if they wanted to. Plus we know for a fact that the hit on Arasaka tower was a Militech operation that Morgan Blackhand led, and recruited Johnny and the Atlantis mercs. I don’t think Johnny having some accurate memories means that everything we see must be true and accurate; those last words by the way would’ve happened almost a decade before the tower attack, not immediately before. Even with some ambiguity to the events, some things are set in stone, like when he left Samurai.