Whats so difficult with "think first, then execute" ?
Archiving is nothing that is made by passing by. You have to have a project, project teams, decisions have to be taken about what is to be archived and where it is to be stored, how it can be accessed etc etc. Such project teams are built to have experts from the business who are knowledgeable about what can be archived, what is not needed anymore for daily work, IT experts who know the dependencies between then archiving object, even lawyers or external auditors who can help you to know the legal impacts, and certainly people from your Basis team who will give you input where to store the data. And all this (and many more) has to happen before you even do a first execution in a productive system.
Computer systems are not much different, create a file in your PC and save it in a personal folder A. Create a link to this file on your desktop. Now move this file from your folder A to folder B. And finally execute the link on your desktop.
Result: the link goes nowhere and you can't open your file. While windows gives you still an option to execute a search, the same is not available in SAP.
the place in your file system is an interim place, of course there should be enough space and it should be restricted with authorization settings, but frankly spoken it does not really matter since you are only done after your stored the files in content repository. And this final step is actually moving the file from the file system to the Content Repository, hence the interim storage in the file system is empty after the file is moved.
If at some day you decide to move the files somewhere else, then you usually bring them back from the CR into the file system and store it then into a new CR, this would be the normal way.
If you decided that the file system is the end, then you should make up your mind first and define the right destination directly.
However we are in IT business, and I would never say that it is not possible at all to move a file into a different path. It might not be the SAP design, and it is not possible for endusers, but there are options for IT people to change table entries to have SAP look into the right path.
But this is then on your very own risk and you have to do a thorough test.