For instance Heroku still doesn't provide straightforward support for wildcard domains under SSL: https://devcenter.heroku.com/articles/understanding-ssl-on-h...
There is myriad of other cases, basically every time you diverge a bit from the 80% path, you're in for a treat and will deal with all the intricacies of SSL management.
The end game is first-party support for automatic HTTPS in all web (and other) servers. It is happening (e.g. mod_md), it's just going to take time. For example, to get it packaged for all distributions.
For shared hosting, if you ignore the few providers at the top who are either CAs (e.g. GoDaddy) or are in contracts with CAs (e.g. Namecheap), the overwhelming majority of them are already providing free and automatic SSL for all hosted domains.
There's still a need for certbot et al when you have multiple services (e.g. web and mail and XMPP) running on a single domain name. In fact, I actively avoid servers that insist on doing ACME themselves because it breaks my unified ACME process.
If the middlebox can't see inside your flow because it's encrypted it can't object to whatever new thing it's scared of this time whether that's HD video or a new HTML tag.