As you said if the plugs don't wind up in the track area it doesn't matter that the material isn't the same as the coverstock.
There is some change to the weight distribution but generally speaking one plug and re-drill has a negligible effect on the ball reaction. Most of a balls reaction is due to the composition and texture of the coverstock. The little bit of change in weight distribution due to plugging, while probably measurable with C.A.T.S. equipment, wouldn't be visible to the average bowler.
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