use this target to measure what is happening:
Print it with the "actual size" setting of your .PDF printing system. ENSURE that the small squares are 1/2" across, the whole chart should be 7.2" across from one thick line edge to the opposite one.
From one point of the large orange diamond to the opposite point there are 137 mm's (5.4") which, at 25 yards (from target to turrets) translates to 6 miliradians.
If your scope is true at highest magnification, then when you set it to whatever that is, it will calibrate with the chart on the horizontal "wire".
If not, then move the magnification till the large orange diamond spans 6 hashmarks at 25 yards and you will know that at that magnification, your horizontal marks are "true mils" and the marks on the vertical "wire" are 2, 5, 8½ and 13 MOA's. Mark the point in the mag ring.
As Bill Price says, it is not a big problem. But life is so much simpler when you can start from solid information and at least an initial trajectory proposal from a good software.
If you KNOW at what magnification your scope is true, then you can use the second focal plane characteristic to your advantage by making the marks whatever is most useful to YOUR trajectory.
You can have another "DOPE" sheet for standing shots and reduce the magnification to allow you to take your shots with less stress.
IMHO, ignorance is not bliss; but I emphasize: it is just my humble opinion.
Hope you go through the exercise and keep us posted!