Wordpress Multisite - Possible to configure letsencrypt without separate apache files?

Hi,

This question was answered:

SNI is about your server config, not what an SSL issuer can do.

You don't need to intentionally setup SNI, the thing you want is setup different ssl hosts.(however that is not what you wants to do if you don't want to set up vhost each time)

So, my suggestion at your situation right now :take advantage of SAN names LE can issue (Up to 100 domains). Which means only use one cert that contains all your client domains.(Or you probably need to setup virtual hosts for each domain).
**Warning:**If you use this method, remember to add each new san to your existing vhost.

Actually, the ultimate (personal) suggestion is to get a CPanel and add domains under one account, use letsencrypt automatic SSL. (That's easier but costs more each month)

Thank you and good luck,

Steven Zhu