At close range, 50-100yds, you're not likely to find much difference. Generally, all full power ammo shoots within a couple inches at 100yds. Every once in a while, you'll find a lot or load that just does not agree with a barrel and goes wild. IME this is the exception, but I have had it happen. With high power rifles, trajectory differences are minimal and not terribly relevant, you're focused on offset due to barrel harmonics and black magic.
At 2-300, you may still hit steel, but it's questionable whether trajectory or offset is to blame for a miss.
You really need to shoot each load on paper, at least at 100yd if you have a chrono, or 100 and 2/300 without. The best you can do is verify that load B shoots Xup and Yleft, and either do the math based on drop and known BC (from firing at a further distance), or use the velocity from the chrono to plot trajectory.
These plots can then be compared fairly from the same assumed zero. Then the zero distance can be adjusted with each one to achieve Maximum Point Blank Range, or whatever else you may wish to do.
E.g. if you use two different bullets, you may find that A is best used with a 50/200 zero, but B is best with a 36/300. Since actually zeroing at 300 could be difficult due to wind or range restrictions, you can consult the tables and reference that with A @ 50/200, it will be 1" high at 100yds, and that B @ 36/300 is supposed to be 2.5" high at 100. Now go fire and zero your rifle for A. It now hits 1" high at 100. Fire B. B actually hits 3" low. Now you know, that if you wish to use B, you need to come up 5.5" at 100, or 5½MOA.
To throw in a horizontal offset, do the same, but no real math is needed. Just fire a group of each in good conditions or a well measured wind (accounting for wind drift). You then know for later that with a zero for A, B needs however much offset.