> Why does LetsEncrypt expire the cert while the acme DNS entry is still there?
That's like saying "why does the government expire my passport/driver's license when I haven't changed my name". That's not how it works; the document is stamped valid for a specific amount of time, and you get a new document with a new expiration time when you renew it.
The certificate from LE will expire automatically 90 days after it was provided, that's why you need to renew it before the 90 days are up.
If you hate setting up automated certificate renewal, you can still get longer-lasting certificates from paid certificate providers. It used to be that you needed to pay a company to generate a certificate for you every year, now you just get the option to have a free one every 90 days.
> Also, why not support file based auth in .well-known/acme-challenge/... for domain wide certs
An ACME challenge file on a web server proves that you control a specific server at a specific domain, so you get a certificate for a specific domain.
A DNS entry proves you control the entire domain, so you (can) get a certificate for the domain.
By uploading a file to tekmol.freewebhost.com, you haven't proven that you control either .freewebhost.com or .tekmol.freewebhost.com. You have just proven that you control tekmol.freewebhost.com.