I wouldn't say they were grown in identical conditions at all... Their growing environments and outside stimuli couldn't have been more different.
The smaller plant that is twice as old as the larger plant, was in a growing environment, correction, it is still in a growing environment that is half the size of the larger one. The container with the soil/soiless mix is the growing medium and a huge factor that is part of the environment - the smaller the pot the smaller the plant. The plants growth most likely became stunted due in large part to being root bound in a small container...
More over, you TOPPED the smaller, most likely root bound plant.... when you top the plant you are externally manipulating the Auxins of the plant... Auxins are the plants hormones that control the plants growth.