While not having tested the auto-configuration without SNI, I don’t see any reason why you shouldn’t be able to issue certs for those domains. You might need to use certonly mode with webroot or http-01 auth and configure the vhosts yourself, but apart from that it should work out of the box.
I’m not 100% certain how this will work with SANs, because there have been problems with the webroot method in that regard (same webroot for all domains, can be solved easily) and it is possible (while unlikely) that the client will complain about the domains being hosted on different machines.
Your best option is probably to use the reverse proxy method explained here LE client needs to bind to port 80, which I'm already using
OR
Simply issue one cert for all domains regardless of their IP.
If you issue one cert for each domain separately that should work as well, but results in more work.