I don't think there is anything wrong or dated with running scripts from the command line, I do it quite a bit, and I think lots of other folks do as well. Sometimes I find integrating scripts into the ArcGIS ecosystem (Python toolboxes, etc...) not worth the effort.
Anyhow, if you are running scripts from the command prompt or directly from an interpreter, i.e, not through ArcGIS client, then background processing doesn't really exist. If you have 64-bit Background Geoprocessing installed and run the script using the 64-bit Python interpreter, then the script uses 64 bit tools. If you have 64-bit Background Geoprocessing installed and run the script using the 32-bit interpreter, the script uses 32-bit tools. The Background Processing setting under Geoprocessing options applies to running scripts within the ArcGIS client (ArcMap, ArcCatalog, etc...)