Hi Julie,
You're correct - unfortunately, AtoM's physical storage module is very basic at present, and there's no way to organize containers and locations hierarchically. I think that if the workaround you're trying is meeting your needs, then yes, you can absolutely work that way in AtoM!
As for other ideas... your best bet is likely to continue getting creative with how you use the location and container naming conventions to capture the information you need. For example, you could instead try adding 2 different containers to each, and try treating the stores as containers. If you know you need to combine 2 entries (one with store, the other with row-bay-shelf) for the full location information, maybe that will still work in terms of reporting?
Honestly, whatever works best for you! We would love to improve the physical storage module in AtoM, but it will require community support for us to be able to overhaul it.
In the meantime, we do have some reports for physical storage that might help you find what you want. See:
Cheers,