Dear Tobias,
as you have noticed, SPM does manage all paths below the top level SPM folder on its own. One reason for using the batch system and its related *cfg*/*run* code is that everything you set up in a batch should be documented and reproducible on similar SPM installations. If you can't or don't want to change SPM behaviour for your whole network install, it might be a good idea to create a SPM toolbox with all the changed files (using different filenames, if possible). As a minimum, you will need a small *cfg* file for your toolbox that collects the changed batch configs in a cfg_choice object.
Obviously, you will need to have your toolbox installed on your network filesystem. Then, you will have the full advantage of using either standard SPM or your toolbox code.
Hope this helps,
Volkmar
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