Unity: We have to charge for every install because we only see totals. Also Unity: We can tell which install is which, so you won't be overcharged.
My guess is that they have some heuristics and wil compile a bunch of data based on everything they can get their hands on, could be number of reviews, data from the platforms or whatever. Coupled with their own anonymised analytics they will have a number with some degree of accuracy.
I would never have predicted this move in 1000 years. Tracking download seems insane. Like a fake good solution that made sense in the infinite-meeting culture but for which no actual analysis was done. Hell, I would have expected Unity to try to monetize its industrial solutions and to leave mid-sized game studio alone.