it's pretty tough to restore alias's reliably. If there is a repository of the same type and with exactly the same name, then it may be feasable. For individual teachers or small Moodle sites it could be done, and this kind of situation is prbably what you have in mind when you ask your question.
However, Moodle installations can be huge. Mega-huge! Furthermore, "repositories" are not just "File systems", "Private files" and "Legacy Course Files". In fact, in my opinion those seem to be secondary to the main intention of Moodle 2.x files which is online repositories such as DropBox and GoogleDocs and friends. I don't really know what happens when we link to those kinds of repositories, but I imagine it would quickly get complicated if TeacherAAA created an activity lnked to her DropBox account. Later the course was backed up by AdminBBB who wanted to move the course to a new server. When AdminBBB restores the course on the new server, should we let him link to TeacherAAA's DropBox account? Maybe yes, if he is restoring on a school server, but maybe no, if he is attempting some terrible deed on his local server at home. These kinds of problems make it tricky to leave links to any and all repositories.
Perhaps we could just restore links to File Systems, Course files and Private files. I don't know. You could try asking on the tracker. Maybe there is also something in the Moodle "road map" about this.
I will be working more on the TaskChain backup in December, at which time I will have a better idea of whehter TaskChain can attempt to relink files. At the moment though, I fear the links are lost during backup, so it may be hard to recreate them.