Chief Ray
If there is no vignetting, and there are no aberrations, the chief ray is defined to be the ray that travels from a specific field point, through the center of the entrance pupil, and on to the image surface. Note that without vignetting or aberrations, any ray passing through the center of the entrance pupil will also pass through the center of the stop and the exit pupil.
When vignetting factors are used, the chief ray is then considered to be the ray that passes through the center of the vignetted pupil, which means the chief ray may not necessarily pass through the center of the stop.
If there are pupil aberrations, and there virtually always are, then the chief ray may pass through the center of the paraxial entrance pupil (if ray aiming is off) or the center of the stop (if ray aiming is on), but generally, not both.
If there are vignetting factors which decenter the pupil, then the chief ray will pass through the center of the vignetted entrance pupil (if ray aiming is off) or the vignetted stop surface (if ray aiming is on).
The common convention used is that the chief ray passes through the center of the vignetted pupil, while the principal ray passes through the center of the unvignetted stop. OpticStudio never uses the principal ray. Most calculations are referenced to the chief ray or the centroid. Note the centroid reference is generally superior because it is based upon the aggregate effect of all the rays that actually illuminate the image surface, and not on the arbitrary selection of one ray which is "special".