No, you won't be charged retroactively for previous downloads. But the change does retroactively affect games previously released on Unity.

So last year you made decisions on your game's price and revenue model that are no longer true. if you made your small game free to play with microtransactions and its had more than 200,000 installs you're probably shitting yourself. Unity will be charging $0.20 per install even if it's to the same device multiple times. A million installs of your game is you having to write a check to Unity for $160,000 for installations alone.

So your microtransactions game now must average a spend of at least $0.20 per install, plus per seat licensing of Unity, plus your overhead for it to even begin to make a profit.

And Unity has said that multiple installations on the same device will all be charged. So it's inevitable that script kiddies with bad attitudes are going to install a game thousands of times. Unity has said you can appeal this type of behavior, but that puts the onus of detecting and reporting this stuff on the devs, further increasing their workload and risk.