Yes and no. Although a flautist can vary intonation using the embouchure (although a lot less in the third octave than in the lower octaves), the correct placement of the stopper is critical to getting the harmonics in line, which in turn is very important for the intonational tendencies of the third octave.
I doubt you want to know the precise acoustics, but without that little bit of "dead" space above the embouchure hole the third octave would be about 25% sharp, as it is on vertically blown flutes like the shakuhachi and quena (and would be on the recorder if you could play a third octave).
To bring the harmonics into line, the distance from the center of the embouchure hole to the stopper should be the inner diameter of the body tube of the flute. If it is shorter the third octave will tend to be sharp, and flat if it is longer.
Different embouchures actually require slight adjustments to this distance based on the length of the airjet (player's lips to embouchure-hole edge), and so there is some adjustment room here for players' intonational tendencies as well, but it shouldn't stray too far from the ideal.
It is a bit like a sax player who "bites up" on the mpc, raising the pitch: pulling the mpc off the cork will lower the pitch, but at the price of screwing up the overall intonation of the horn.
Toby
