However, I believe I have found the source of the problem. Apparently, the iCloud-synced keychain maintains a copy of deleted SMTP servers even after they are "deleted" in Mail – but they are hidden in the "normal" view of Keychain Access, which prevents them from being found and deleted directly. As a result, they keep being added back to Mail's default SMTP servers whenever syncing of keychains is enabled.
To find them in Keychain Access, you have to enable "View -> Show Invisible Items" and look for items named "com.apple.account.SMTP.asynchost". (It may also be necessary to find items named "com.apple.account.SMTP.accountsync".) Check which ones contain the offending STMP server (at this point the Find field should work to locate them). Quit Mail, then delete them. Enable keychain syncing. When you re-launch Mail, the SMTP servers should finally be gone.