Within the limits of what you have to work with, there is one practical test you can do that will partly answer what I think is the main question you are trying to answer.
1. Sight rifle in for whichever your normal zero distance is. (Let’s say 91m/100yd)
2. Enter the ballistic data into the app for a (368m/400yd) shot. Dial according to the app data and shoot a group at this distance.
If the group is level with the aiming point, you can have a reasonable degree of confidence in data and dial at further distance. If it is not level, the next step is to work out if this is due to dial, calculator, other, or some of each.
To answer the question at the end of your post, the two ballistic calculators that you have used should both be able to reverse engineer your data if you enter a 600m zero and then look at the trajectory chart. Allow for some dispersion due to scope height etc but it should give a 91m/100yd elevation of ~33.5cm if your original calculation for a 600m dial up was based on a dial starting point of 91m/100yd.
Also note that the math only proves the math. If the math indicates the same elevation through two separate mathematical methods, it doesn’t prove what will happen in practice it only proves that both methods are as valid as each other.
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