Given Magento 2’s enterprise ambitions, it wouldn’t surprise me if most stores are routing their transactional emails through a seperate (or a series of seperate) email systems. Because Enterprise™. However, if you’re sticking to Magento’s default email system for the password reset, order thank you, sign up, etc. emails, then you might want to check out Daniel Sloof’s Custom Email Theme extension. This extension allows you pick any installed Magento theme and have Magento use it (instead of the Blank theme) for transactional emails.
It’s odd to see this sort of fuctionality missing from Magento’s core more than two years after release.