Some of the choice can be convenience. If all your tooling has the same shank, then the same collet or Weldon holder can stay in the spindle, saving lots of time and effort. Of course, running a 3/4" capacity drill chuck with a 1/4" shank would be silly, also the reverse of that. Straight shanks also have no need to be longer than the gripping surface that holds them. Shorter shanks make for quicker tooling changes, and can often be easily changed in tight setups without moving anything. Changing collets takes more time. For some jobs the added strength of integrated shank tooling can be a good thing. For accuracy, either can work, and if the high sides of the individual components are marked on them, accuracy can actually be gained by the additional interface.