So, I still don't trust Unity, and wouldn't in good faith advise its use moving forward given that there's no way to know they wont try to pull this again in the future (especially given that John "Pay a Dollar to Reload" Riccitiello hasn't resigned in disgrace as CEO). However, I feel there's a part of the letter that you've left conspicuously out of this response.

But you still never answered how we can trust the install numbers that your tool supposedly collects

They addressed this, see this copied paragraph, emphasis mine:

For games that are subject to the runtime fee, we are giving you a choice of either a 2.5% revenue share or the calculated amount based on the number of new people engaging with your game each month. Both of these numbers are self-reported from data you already have available. You will always be billed the lesser amount.

This also addresses two your immediate followup concerns, piracy and install-bombs -- always being billed the lesser amount would act as a safety valve against unprofitable install spikes, on top of the fact that using licensee-reported numbers allows for agency on the part of the licensee to screen for malicious activity before being billed.