The player doesn't know that the villain is their father. That is part of their backstory. Since it is not known to the player until it is revealed, it is a secret part of his backstory.
I know you'll have something to say about when the GM determines that - is it preplanned or is it made up on the spot. Just like what I was saying about a "meaningful" choice being a red herring in my post about...illusionary choices (have no idea what to call it at this point!), I think that whether the DM knows about it at the beginning of the campaign, a couple of sessions before it's revealed, or even a few moments before he reveals it is irrelevant in whether it's classified as "secret" backstory.
I would also be surprised if there aren't points in Story Now games where something like that might occur to the GM during a session, and they realize that it's not the right time to reveal it, so it waits for a later time, even several sessions later.
But really, the point is that Eero specifically points out backstory elements that the player themselves does not know and are not authored by them. That to me = secret backstory.
There are several posts that I could use to initiate this conversation, but this is as good as any (as there are several relevant bits).
I've recounted a few times one of my favorite moments GMing Dogs in the Vineyard (the best game from The Forge and in competition for my favorite game period).
One of my players chose a Relationship at 1d4 with his brother which was (something like) "my brother raised me when our parent's died...he's my hero." 1d4 is the worst die possible. It doesn't signify the closeness of the relationship, however. It just means that when the PC's brother is involved in one of our conflicts, it will serve to complicate matters rather than help.
This is a signal from the player (a). So I have this to work with up front.
So the PCs have struck out to a town on the periphery of the territory that attracts drifters, desperadoes, and general rabble-rousers. It is having all kinds of troubles because of it. There is a reason for this traffic; a powerful rancher outside of the territory is subsidizing a brothel. Now prostitution is very much against the faith.
When the Dogs arrive in the foyer of the building, the PC mentioned above sees a familiar hat on the coffee table; his brother's. The other Dogs know the hat too and they're all taken aback. The relevant PC says with absolute certitude something like "if the man who took this left him a shallow grave...there is going to be hell to pay."
From this I learn:
b) the PC is willing to risk a hell of a lot for his brother (fights with multiple gunmen are lethal) including potentially his oath as a Dog (cold-blooded killing may be in the cards here...let us find out).
c) the player has expressed interest that the hat signifies something bad potentially befalling his brother (and a revenge scenario perhaps arising from it) rather than his brother's heroic status being on the line (eg what if his brother is sinning in the brothel?).
So, given (a) and then (b) and (c) above, what is an appropriate Story NOW approach:
1) I shouldn't have made the hat his brother's. I mean...what are the odds? That isn't very realistic. A better choice would have been to have just made it a dusty hat smelling of sweat, booze (sin), and gunpowder (possibly sin). That is still very relevant to the general premise of the game (vulnerable, gun-toting Paladins risking everything to mete out justice and protect The Faith in a Wild West that never was) if not the specific thematic material signaled in (a).
2) Yes, go with the brother's hat, but even if the fiction hasn't established the nature of the hat's place there, if I thought it would be interesting to find out what happens if the brother does indeed reveal a serious moral downfall and sin against The Faith here, I should keep it that way and ignore (c).