Let’s Encrypt can provide multiple certificates for the same domain (in case one is lost, I suppose), but certbot tool is tuned to handle one certificate for one domain. So is FreedomBox’s code handle certificates.
If you wish to play around with special certificates for specific apps (or for hosts on the local network), then subdomains is the way to go. If you own a domain by purchasing a name with domain registrar or by having a free domain from ddns.freedombox.org, then you can have unlimited number of subdomains. See FreedomBox/Guide/ExposeLocalService - Debian Wiki for information on how to setup subdomains. This guide also talks about setting up TLS certificate on FreedomBox while forwarding unencrypted traffic to another host hosting a service on the network.