Wood beam

"Problem is the garage door mounting hardware is in the way"

Is this the garage door header? If yes I wouldn't use it for anything other than its intended purpose which is to hold up the Roof/Gable End and provide lateral support for the garage door. Less you want to pull the roof and wall down.

As far as the hole is concerned; when the lumber is graded at the mill the diameter and proximity of the knots determines the usable grade ie.. 2KD 1KD 2DKD ect.. The board or beam as you indicate is only as strong as the largest knot hole allows. If you see same size knots(3/4") check the distance between them and proximity to the edge, use that info as you guide in determining weather the hole is detrimental to the effectiveness of the beam.