I think this is expected. The "Arduino" chip on the Yun is an ATmega32U4, and similar fixes involving Serial port are often needed for other types of arduino based on same chip.
This is a known problem.
When developing a sketch and using debug messages, then the Serial port should run before continuing.
void setup()
{
Serial.begin(115200);
while( !Serial); // wait for Serial
Serial.println("Debug Message");
}
However, if the Serial Monitor of the Arduino IDE is not opened, then it waits forever.
You could wait for 30 seconds and then continue. But if the Serial port is not opened, then you should not use debug messages to the Serial port.
You could also use debug messages that can be turned off with a #define.
This is not a problem for a Arduino Uno, because it has a separate usb-serial chip.