Well, bug closed, but issue not really resolved... It turns out that the config for freedns.afraid.org is "special" and doesn't fit into the standard fields presented in the FreeNAS GUI. It's possible to make it work though. So for future reference, this is what works for me:
Provider: freedns.afraid.org
Domain Name: yourfirsthost,MD5HASH ip4 (note the comma and the space and that technically "ip4" is optional)
Username: guest (not used, but should be filled in)
Password: guest (again, not used)
Confirm Password: guest
Update Period: 3600 (1 hour)
Forced Update Period: 86400 (1 day)
Auxiliary Parameters: --alias yoursecondhost,MD5HASH ip4 (repeat for additional hostnames using the same IP address)
Get your hash: Log into your account on freedns.afraid.org, click on "XML API" and view the magic incantation. It should be obvious which part of the incantation is the hash.