As far as I know, it is still the case that the built-in cPanel/WHM AutoSSL functionality only supports 1 AutoSSL certificate per cPanel account.
Last I heard, the suggested workaround for dedicated AutoSSL certificates was to convert subdomains/addon domains to their own cPanel accounts. Though this is now a fairly painful solution due to the recent licensing price hike.
As cPanel maintain the Let’s Encrypt AutoSSL plugin, you can get the most accurate and up-to-date info from cPanel support or on the cPanel user forums.