Create a bookmark with an SFTP connection, Username and Password (don't check "Use Public Key Authentication"), and check the "Add to Keychain" checkbox.
Open the connection and exit Cyberduck. (The password is now stored in the OS X Keychain.)
Open Cyberduck again and go to that bookmark. The "Login failed" dialog pops up ("Exhausted available authentication methods. Please contact your web hosting service provider for assistance."), prompting for the "Private Key Passphrase", with the "Use Public Key Authentication" checkbox automatically checked, ~/.ssh/id_dsa shown beneath. (The site I use allows SFTP connections with username/password, but no PKA.)
If I move away my ~/.ssh folder (which contains PKs for other sites) temporarily, Cyberduck uses the stored password and logs into the SFTP site without error.
The bookmark should probably memorise the preferred authentication method for the site and not switch to PKA only because a ~/.ssh/id_dsa file is present.
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