This conundrum rings a bell with me. I think Lantirn may have hit on the relevant issue that in rare cases could favour the intersection departure. IIRC, it's a close-in obstacle that ceases to be an issue if the take-off run is started beyond a certain point on the runway. Could be tall trees or structures close to the side of the runway, such as a control tower. So it's a NTOFP limitation, not WAT.