Lets Encrypt SSL not implementing on autocreated Sub-domains on Multi-Tenant Project

In theory, sure! However, it all depends on what your software can offer you.

Looking at your situation with randomly added subdomains to your domain, you might benefit from a wildcard certificate. However, while a wildcard for *.example.com would cover e.g. user.example.com, it would not cover another label deeper like www.user.example.com.

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