If the plot hole to which you're referring is that canon!Voldemort could have used his extreme skill to get the Philosopher's Stone, instead of going for Horcruxes, the idea that I always got was that the Philosopher's Stone extended life, by preventing aging, but Horcruxes prevented death, by tethering the user's soul after their body died. If someone had killed Nicolas Flamel while he was regularly using the Elixir of Life, I don't believe it would have helped him. Canon never says how Horcruxes deal with death by old age, but if it worked the way Voldemort's death worked, then a person who died of old age would get a ghost-form that could then in principle be reincarnated as Voldemort was. (Which is another highly evil piece of magic. What is it about life-extension that people think is evil?) It's never mentioned whether Voldemort's new body would ever die of old age.