I am having a difficult time figuring out what you are questioning in here.
I think you are just looking too much into conventional and practical flow of current. The main focus of BJT is to think of them as a diode for the control gate. You need a certain amount of voltage from the base to emitter to complete the conduction path (usually 0.7V either positive or negative depending on NPN or PNP) and allow for current flow. Once the BJT is on, the current flowing into the gate controls the current that flows through the junction. It is essentially a very small resistor so it can support current flow in either direction with a gain that is defined by the part. Please let me know if this helps or if I answered the wrong question.