But isn't it stated that in the absence of direct control from Phillipa, Sile controls the dragon?

I did the same Iorveth / Triss ending as the OP and also wondered at the purpose of finding the dagger at this point in the game.

I doubt we will need to wait until TW3 for this to be resolved. Based on the way Act 3 ended, I suspect there will be TW2 DLC or an expansion that will involve Geralt having to find Saskia for some reason. The dagger will then allow Geralt to break the control spell,and hopefully clear up some the loose ends and the politics in the Pontar Valley.

Sile acts as if she is in control of the dragon. But that doesn't explain why the dragon still has it in for you after Sile's teleportation mishap, unless Philippa is still pulling some strings.

I guess Sile and Philippa share the control of the dragon. Philippa says at one point that if she dies, Saskia will remain a spellbound monster forever and will just destroy everything.

So I guess when Philippa and Sile both die, Saskia just goes off the deep end, the unfortunate victim of lesbomancy that she is. Insane dragon ahoy! I felt rather bad putting her out of her misery (she appeared to have regained her wits in the end), but then again, I owed her a good ol' stab after she almost ate me in the prologue.