Soy milk does not naturally contain a lot of calcium; it is added.
Since you are looking at a website rather than physical products, I would guess that one whole milk has the new nutrition facts panel and one the older one. The amount of calcium for %DV went up from 1000mg to 1300 mg. https://www.fda.gov/media/135301/download
Are they different types of milk? If they’re not dairy, they are likely to have different numbers because of the processing. Some use more water, some less. If it’s dairy, the filtration process and what the cows eat can effect the quality of the milk
In terms of real milk. Yes. It varies pretty fairly based on the animals feed and management. Better conditions and nourishment = better nutrient content. This also goes for the least processed milk since most of it is overly treated.
As for fake milks, they are not very nutrient dense. So to compensate for this (like in any highly processed food) they fortify it with vitamins and minerals (although usually it’s poorly bioavailable forms anyway).
My suggestion? Stop obsessing over specific nutrient differences. Buy high quality food, buy least processed and drink/eat away.