I see your point. So, then I should do this:

$tmp = $data[$gid]->{$id};
$tmp->[$element_num] = $element;
$data[$gid]->{$id} = $tmp;
[download]

I haven't tested this yet, but while typing it, I noticed that with the $tmp assignment, that I'm pulling all of @{$data[$gid]->{$id}} into memory, partly obviating the advantage of the disk-based tie. It would make more sense then to generate the entire @{$data[$gid]->{$id}} array in memory and only save it when all the elements are computed. Is that correct?