Is it possible to use the spamc/spamd pair by invoking spamc with a per instance refernence to a list of customized local.cf files?
No, local.cf level files are parsed only at the start of spamd. By the time spamc is called, it's too late.
I would like to have different rules on a per destination domain basis. Is this possible?
You have 2 options:
1) run 2 spamds, each with different listening ports specified with -p, and different --siteconfigpath's. Select which one you use by what you pass to -p on the spamc command line.
Advantage: easy, and still allows per-user customization. Drawback: doesn't scale well, wastes memory
2) if you don't have per-user customization, you could create 2 user accounts and pass the appropriate username to spamc -u. You'd also need "allow_user_rules 1" in your local.cf, which is not a risk if no untrusted users have local accounts that can log in.