I can use the "home name" directive to change the name of the user's home share, but if it doesn't contain the %u variable, the directive is ignored. I end up finding this in the syslog:
Sep 6 21:02:19 ip-10-8-0-215 afpd: home name must contain $u.
Note that the inability to have the same name for all users' home shares (e.g. "Backups") breaks Bonjour discovery of Time Machine shares. The name of the share to connect to must be part of the service advertisement (reference), so it can't be different for every user.
Bonjour discovery isn't a huge deal for initial configuration, but it's a huge help if you ever need to restore a system completely (rather than individual files). Without it, you have to use Terminal to mount the AFP share beforehand from the boot CD (or recovery partition) environment, which is unpleasant.
This is something that was possible pre-3.0.