The folder is specified via:
firmware/export/config-iaudiox5.h:150:#define BOOTDIR "/.rockbox"
and
apps/settings.h:50:#define ROCKBOX_DIR "/.rockbox"
although I've never heard of anyone changing this - but it maybe possible to ROLO to a build that has a different value? Grepping through the code there are a few odd places that use hardcoded values (dircache, logf and several plugins).
EDIT - hah, I forgot about all the buildscripts - it'd be a fair amount of work.