The above link also explains how reference code inheritance works in AtoM. In essence, a full reference code for an Item that is part of a hierarchical description would be made up of:
So if you had a repository in Canada with an institutional identifier of REPO, and a heirarchical description with basic identifiers at each level (e.g. F1 for fonds-level, S1 for series level, f1 for file level, and i1 for item level), your inherited reference code at the item-level might look like this:
Here's the example image in our docs, so you can see what I mean:

In AtoM 2.1, the setting for reference code inheritance will also affect how identifiers export in the EAD. If you have inheritance turned ON, then when you export, the full reference code will be included in the <unitid> element for each level. So for our item-level description, it might appear like this:
If the inheritance is turned OFF, it will only export the identifer for that level, at each level of the description in the EAD.
By default, AtoM will use a dash (e.g. - ) to separate reference code identifiers - but this too is a configurable setting via Admin > Settings. See:
As for supporting physical retrieval:
AtoM does have its own separate, albeit minimal, module for managing physical storage. See here in our manual for more information:
At present there is nothing in either the identifier field, or the physical storage module, that would allow for anything more sophisticated, such as linking to an external location managing or retrieval application.
However, I do know of institutions who structure the identifier in such a way that it reflects their physical storage - in fact I used to do this at UBC's Rare Books and Special Collections when I used AtoM as an employee there. I've outlined the approach we took here:
Hope that helps!
Cheers,
How do you structure your reference code (ISAD G). And does your reference code support physical retrieval?
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Cheers,