That's pretty much what I think as well. He'll probably brush that line off with: "Forget it, I remember."I feel like you're reading far too much into Capaldi's line.
Do you know how to fly this thing is more of a joke than any sort of foreshadowing. It's a running theme with the doctor regenerating that he goes through a period of confusion, sometimes intense, as he adjusts.
It's the whole fish sticks and pudding thing.
Edit: He also lied through the truth field telling Clara that he wouldn't send her away again... then boom, sent her away.
Conversely it's possible he hadn't piloted the Tardis in 1000 years; 300 had passed and he hadn't aged all that much and by the time he regenerated he was ancient. Might take him some time to remember how to do it.