First, the bare meaning of the words:
You might think you will never be a top student.
This is not necessarily so.
Three parts to understand the second sentence:This, not so and necessarily.
This is the proposition that you will never be a top student.
If we just said This is not so we contradict the proposition, we assert you will be a top student.
The addition of necessarily allows for uncertainty, ** This is possibly not so** or to state it positively it is possible that you might be a top student. Note that there is no explanation of this positive assertion, just a statement of opinion.
So, your statement 2). is not quite right, we are talking about possibilities not certainty.
Your statement 1). follows from the reasoning above. We assert that you may possibly be a top student, therefore we believe that your current thinking is wrong.