The TORA quoted for an intersection departure is calculated from the intersection of the extended downwind edge of the relevant taxiway. So if you follow the TWY centre line out and line up you will always be short of the quoted TORA (admittedly not by much although if it is, say, a RWY 01 A6 departure at BNE it could be a couple of hundred metres or so because of the diagonal angle.)
Mind you this is no different to full length as once you line up the short part of the RWY underneath you and behind you is also part of the TORA you are working with.