you want the entire substrate to get wet.. you don't pick the volume. the composition and volume of substrate dictates this.
if you have enugh perlite or simila, then the roots will be fine. it is a poor habit not to irrigate until entire substrate is wet.
if the pot is too big, you do a smaller column of watering around the seedling but you still want that moisture to go all the way down. it has to do with avoiding superficial roots. you want the top to dry faster than the inner/bottom volumes, not the other way around, which is what happens if you water with insufficient volume.
use close to 50% perlite in soil. 30% in coco. you'll never "overwater" it.. in any common sense context. if it's too wet in root zone, it is you soil composition's fault not the watering.