You know what, I agree completely. The best ending is after all a part of the games narrative & it confirms that in the end Dracula was not destroyed for good even if a character from the manual or the narrator says so.
Look: what's happening here is that the game's ending conflicts with what is written in the game's official manual. In fact, it seems to conflict with itself -- right before that confusing "hand out of grave" scene, you can clearly read: "The encounter with Dracula is terminated. Simon Belmont has put an end to the eternal darkness in Transylvania. His blood and sweat have penetrated the earth and will induce magic and happiness for those who walk on this land." After that, you'd expect closure; it doesn't quite sound like "Dracula will soon be revived", does it?
But now look at the "Good" ending. Here's the text: "Although the confrontation between Simon and Dracula has concluded, Simon couldn't survive his fatal wounds. Transylvania's only hope is a young man who will triumph over evil and rid the city of Dracula's deadly curse." Now that sounds more like it - it seems Dracula's curse has not yet lifted. And perhaps he might even be resurrected... That's far more fitting for what we saw.
So here's where Nagumo's logic comes in: the endings might have been inverted, essentially switching the "good" and "best" ending animations. Thus, Simon would die in the good ending, allowing for Dracula's eventual revival (hence the grave scene). But in the best ending (the intended canon), Simon has triumphs over the curse and lives, having defeated Dracula for eternity. It's far more climactic, and gives an appropriate sense of closure to the story. And it makes more sense.
Of course, that's only a possibility. But, so far, it's the most logical one.
And to put the matter to rest once and for all:
game manuals don't lie. They don't today, and certainly didn't in 1987 -- if anything, they're intended as a
reference. I'll say it again: if there is anything we do know, it's that this ending confusion is the result of an error, and certainly not of an intentional deception. Unless, of course, the developers were utterly incompetent. But that's for you to decide...