The military zeros at 25yds with the small aperture. This gives you a 300yd zero for the small aperture (about 5-6" high at 100yds) and then if you need to shoot under 200yds, you flip to the 0-200 aperture (the large, almost ghost-ring aperture), which is set to a different elevation.
The 50yd zero puts you within 2.6" of your line of sight from 0-225yds (roughly) and you should be dead on at 50yds and 200yds.
If you had A2 sights, the Santose 50yd zero lets you use the 50yd zero with the smaller aperture; but still use the elevation adjustments at longer ranges. However, most flip sights lack elevation adjustments and even those that do have elevation adjustments can't be adjusted like A2 sights to use the Santose zero.
For flip sights with no elevation, my preference is to use the 50yd zero with a same plane aperture (both apertures set for the same elevation). This lets me make hits to 300yds reliably, which is effective for my uses. This way I can use the small aperture for smaller targets close in (say 6" plates at 100yds) but still have a larger aperture for dusk/low-light conditions without changing my zero.
However, if you are just shooting at military style silhouettes (20"x42"), then the 25yd zero with different plane apertures makes good sense since it maximizes your point-blank distance.
Since holographic/red dot sights have no extra aperture, I always use the 50yd zero for these sights since it maximizes the effectiveness of these sights with a flat trajectory in the range they are best suited for (0-300m).
The 25yd zero for red dots doesn't really help with close-in shooting since below 25yds, the height over bore issue on ARs comes into play and you are talking 0.1" differences in point of impact between the 25yd and 50yd zero at distances under 25yds. At distances over 25yds, the 25yd zero for red dots is much more curved and less flat.