Maybe one issue is that Certbot currently doesn’t have a mode to obtain more than one new certificate per invocation. So if you had a list of 1000 domains and you wanted 10 certificates collectively covering those 1000 domains, you would currently have to run Certbot 10 different times.
Beyond that, there is currently no automated method to “rebalance” or “reallocate” domains among certificates, e.g. if you later removed 5 domains from that list of 1000 and added 25 domains, Certbot wouldn’t have a method that could automatically obtain 11 certificates with an allocation that covers the 1020 domains that you now want to be covered.
I can imagine that it could be helpful to have a Certbot mode that says “I want to have certificates that, collectively, cover the domains in domains.txt” and to have Certbot first analyze its current ACME authz list and obtain any necessary authorizations, and second analyze its current managed certificates and perform the smallest possible number of new issuances required to ensure that exactly those names listed in domains.txt are covered by currently valid certificates, and no others. We don’t have any features like that at the moment.