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...you really have 2 zeroes, your line of sight in the scope and your bullet have to cross (zero), this puts the bullet above your line of sight for a time, it then crosses it again on the way down, so really you have 2 zeroes. The close the scope it to the barrel, the less time the bullet spends above your line of sight. Somebody explain this better.
Excellent way to describe the "two zeros" or the difference between the bullet path aligned in the barrel below the scope, and the line of sight your eye sees through the scope above the barrel. On most rifles these lines are from 1 inch to 1.5 inches apart, with some high mounts especially on AR’s up to 2 inches or so.
However, the distance you sight in the rifle determines how far above or below the line of eyesight that the bullet travels, not the objective lens size of the scope, nor how high it is mounted (with normal mounts anyway). I.e. If you sight in the rifle for 75 yards, any modern rifle would never get above the line of sight between the muzzle and 75 yards, but would start an inch to 1 1/2 inch low and rise all the way to the point of impact, where the two lines intersect. Where those lines intersect is the distance at which your rifle is sighted in. As you indicated, with rifles sighted in at 100 yards and farther that happens at two distances: one close as the bullet rises through the line of sight and the other farther away where it falls to intersect the line again. 30-06 big game rifles are often sighted to be on at 25 yards, 3 inches high at 100 yards, and right on again at 260 yards (approximately).
The difference in bullet flight path between a 40mm and a 50mm scope would be tiny on the same rifle. If they fit in the same mounts, there is no difference: the bell for the objective lens is bigger but the center of the tube is in the same place. If you have to use higher mounts to make the larger 50mm bell clear the barrel, it might be as little as 5mm higher, or 3/16 of an inch. That’s not enough to make much difference, and how you sight it in adjusts for the difference.
What makes a much bigger difference to me is how tight and low I can get my face on the stock. I don't shoot as well with my head lifted to see through a high mounted scope, and I prefer smaller scopes that I can mount low.
For most use, I'd go with the 40mm. I have a 50mm, a 40 and a 32mm and I’m getting rid of the 50. The only time I'd go for a 50 mm would be if I planned on doing a lot of sitting and night shooting without a light, and I can do that pretty well even with the little 32mm objective. 50mm gathers more light, but not enough more to make much difference to human eyes except in super high magnification. For stand sitting, a 50 mm is OK. For a walk around and hunt rifle and impromptu calling stands, go for the smaller one. Some extreme long range scopes are 50 mm also, along with high magnification.
For predator and varmint hunting, I don't like my bullet to ever be far above or below the line of sight. The animal targets are small, and sometimes I am shooting through a small hole in brush and want the bullet exactly on my line of sight to go through the hole where I’m looking. Yet I don’t want too much drop out to 150 so I sight my .243 in to be 1 inch high at 100 yards, hoping it will always be within an inch of my line of sight out to 150 yards and especially on the close and medium shots.