Roots grow outward for stability, so they naturally collect at the edges of the container and leave much of the soil in the middle of the pot unused. This will cause slowed growth because the roots may restrict each other. Transplanting allows for a more efficient root mass, as the space in the middle of the final container will be used.
Allowing the roots to collect at the edges of your 1-gallon pot, will ensure a more efficient root mass when transplanting to a 3-gallon pot. Each time you transplant, you can also bury the plant up to the first node or branch to shorten it's overall height.