Reading through the request tracker, I find that there are numerous requests to be able to change partition-specific settings in the configuration file. These include changing volume icons and names, hiding partitions, et cetera.
Implementing these options in the global configuration file on the installation volume would be cumbersome and prone to breakage caused by minor actions. Partitions would have to be addressed by disk and partition number, which would fail horribly if the disk numbering changed. Settings would be applied to the wrong disks, which could cause some very strange results.
Instead, I propose creating per-partition and/or per-disk configuration files. rEFIt could look in the /efi/refit/ directory on every partition it could read for configuration files. You could keep partition-specific information on the partition it concerns and disk-specific configuration (and configuration for partitions with unsupported filesystems) on the EFI system partition of the disk in question.
Partition-specific configuration would survive the partition being cloned or moved on to a different device, and disk-specific configuration would survive the disk being moved to a different system or the disk numbering changing.