There is no “emitter – collector junction” in a transistor. Output is taken across emitter – collector junction dosen’t mean that there is a junction across it.
Think it in this way.
Input junction ( emitter – base ) forward biased : Emitter to lower potential ( ground ) and base to a higher potential than
emitter ( Vbe + )
Output junction ( base – collector ) reverse biased : Collector to higher potential ( Vce + ) and base to lower potential than
collector ( Vbe + )