Hi,
On Leonardo/Pro Micro etc, "Serial.print()" sends to the serial monitor on your pc. "Serial1.print()" sends to the TX pin. So your second sketch is sending nothing to serial monitor. In your first sketch, you are not reading from the TX pin until after the manchester encoded data has finished sending, so you always see zero (or maybe the last bit of the encoded data or a check-bit of some kind).
So that is why you see what you see. Question is, what did you want to see and what are you trying to do?
Paul