Your scope wouldn't have been set up a different way you just thought in a different measurement. If you are thinking in meters then you could have every .1 mil is 1 cm at 100 meters. It is the same angular measurement as every click is .36 inches at 100 yards. Just a different way to think about it. The only time that I ever think of it that way is if I am zeroing and do not have a good reticle. Otherwise, I just measure with the reticle and come over/up what the reticle tells me. This is where I got very confused and I feel like a lot of guys do because they are trying to convert it to inches. I still have no idea how many cm go into an inch but it is really irrelevant when shooting because you simply want to measure your poi in mils and make the correction that way.
I am sure this sounds confusing and I will tell you that I was so confused when going from MOA to Mils! I just had to train myself to think in mils and not try to convert it to a stagnant unit of measurement that changes as distance changes. Use what your ballistic calculator spits out for elevation and for wind, use the wind formula that I have mentioned in previous posts to get the angular measurement in mils. Otherwise, stuff gets really confusing!