For me, the easiest indicator is to compare the "shine" of the two inks. Hold the paper under a light, look closely, and tilt it back and forth until the angle reflects the light off the ink. Printer ink reflects light differently than ballpoint pen ink, so one should look shinier than the other. Pre-printed signatures are usually very easy to spot this way.
Also, I would expect paper signed by a pen to leave minor pressure marks on the paper. Depending on the pressure used by the signer, it might be visible from the back; or you might be able to lightly pinch the paper, slide your fingers back and forth over the signature, and feel the texture of it.
it could be the black line is printed after the autograph ''many in person collectors use just a blank photopaper and let it sign and after that they print for example a movie script front page. just a thought.