They donate 50% of costs to LE at the end of the year[1]. They’re charging for the operational overhead of LE provisioning/serving, not for the certificates themselves.
As someone who has bought one of these LE certs for money, I wasn't (just) paying for the cert, I was paying for convenience. I know I can get it for free and set it up myself. I don't want to set it up myself.
Nice idea, but.. I work with Single Sign-On setups for multiple companies, where both sides of the fence have a certificate which needs to be valid according to well known CAs, and they have to be manually renewed. So a 3 month validity is a non-starter - the cost of buying a 1 or 2 year cert is far less than the cost of manually updating every 3 months.