"Monopoding" the gun using the magazine should not produce any issues with function of the weapon, and should provide a satisfactory zero.
If you are seeing issues with function, first try other magazines. If function issue persists, further troubleshooting may be necessary. A properly in-spec modern AR15 using vetted magazines should *NOT* have any problems being monopodded via just the magazine. Monopoding is also a routinely taught marksmanship technique, and used at high levels.
Question for you experts. When I'm in the prone position with my AR and the magazine is being used for support (tripod: two elbows and magazine form triangle), the bolt does not lock to the rear when the mag runs dry. Magazine used is a Magpul PMAG. What's the problem? Is this normal?
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More likely than not, any POI shift is induced by other factors such as eye-alignment differences when you're seated between bench/table or other positions, and and also the displacement of the sight relationship due to deflection of the handguard to which your front sight is attached. Towards the latter, I am hoping that you did not attach your optic, if you are using one, to the handguard instead of the receiver? That handguard looks monothlic with the receiver, but is not!
In terms of your zero, I would agree with
@Talyn - because of your intended use of the gun within the 100, the 50 yard zero can potentially be easier to use (and remember that the bullet never "rise," -
https://www.thearmorylife.com/forum/threads/suppressor-height-sights.10599/#post-141616), while the 100 yard zero may offer you easier hold-overs if you place more importance on absolute precision:
Understand, however, that these "ideals" are achieved via a "typical" 16-inch gun with the above-listed muzzle velocities (which is again an ideal), using "typical" ammo (again ideal). While your final zero will not differ too, too much based on the above, how your unique gun prints - with your selected ammo - will vary to some degree from this idealized diagram. Printing shots-on-target downrange, "truing" your optic or sights to your setup is the only way to go (especially if you wish to verify the "far zero").