I think I’m sharing the same concern/issue as the OP, but maybe I can help get a clearer, more specific answer.
I have one VPS, with 4 IP Addresses.
I have EE installed on this VPS.
I have 4 Domains, with the DNS of each domain pointing to one of the above mentioned IP Addresses.
I will have 4 websites, each available at one of the 4 domains.
Each website needs its own “Let’s Encrypt” SSL.
Can a single VPS with EE handle all four WordPress websites? Sure!
Can a single VPS with EE handle all four “Let’s Encrypt” SSL Certificates?