OK, I agree. Setting up a licence model where you cannot predict what you have to pay is dangerous. Even if it is no practical problem. (And I am not a lawyer: But changing the terms of use after I installed Unity sounds illegal to me?! Could Microsoft change the terms of use for Word, so that we have to pay 1$ for every Document we create from tomorrow on?)
My not-a-lawyer guess is that the old TOS applies to old versions of Unity - but if you update to the new version, you're stuck with the new TOS. (And Unity is not going to bother telling people that existing, non-updated games are exempt from this whole fiasco.)
I suspect Unity is actually planning to totally ignore everything not distributed through a trackable service, but they don't want to announce that to the public, because then dev companies would be actively looking for ways to dodge their install tracking.