Redeploy Let's Encrypt SSL/TLS Certificate

This is a general setup related question where I don't know what the best approach is. Let's say I have a service where people can sign up and use their custom domains for their public profile, ie. username.domain.com.

I'm currently using RunCloud for server management and attach those domains via API to the application and re-deploy the Let's Encrypt certificate, also via API. Due to the limitation of 20 re-deploys per week, this is not really something I can use on the long run. So I was wondering what the best way to accomplish something like this would be, where I need to allow users to have their own subdomain with SSL encryption.

I'm not really into issuing Let's Encrypt certificates myself on the server (I know there are certain PHP and Laravel packages).

I'd be really happy if someone could give me a nudge on how to do this.