Well, I'd be reluctant to trust a sight-in as close as 50 yards, just because the angular dispersion that close doesn't reveal as much as it would farther out. In other words, only half a bullet width's difference at 50 yards might well turn out to be two inches worth of change at two or three times that distance.
But it really doesn't matter much how or where you measure the bullet's path. It might be one inch high at 50 yards - or 87 millimeters high at a furlong. As long as the bullet doesn't vary too high above the line of sight during its midrange or too far below it after its second crossing of the line of sight, you're good to go.
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