These new Unity per-install fees could hit developers who aren't making money - for example F2P games, free demos, very cheap games (e.g. charity bundles), potentially even pirated copies (if Unity intend to track installs via analytics sent from the runtime?)
In reality, most indies fail and won't hit the 100,000 download threshold or the $100k revenue threshold. But it's a new fee to worry about, and one that gives Unity a lot of 'monetization levers' to pull more aggressively further down the road (tweaking the fees/thresholds)
It's also worth considering that Epic could change the UE pricing model significantly if their sole serious competitor starts to fade into irrelevance...