Hello,
The multiple directories as local root for the datasource is not supported in this moment (and I assume also not in the future) as there can be workarounds for this.
One workaround would be to create a script that creates in a whatever directory, let’s say /mnt/archive/repo with the subdirectories structure like yyyy/MM/dd in which you create symlinks (in the dd subdirectories leafs) to your S2A and S2B products in the /eodc/products/copernicus.eu/s2*_prd_msil1c/yyyy/MM/dd source directoris. This way, you will have a single root repository for all S2A and S2B products without the need of duplicating data.
Concerning zip format, yes, it is supported to ingest .zip products (of course if their internal structure is the correct one). But, it is true that we used it mostly when downloading products but not sure we tested when importing them from local root. Nevertheless, it should work also in this case and if not, you should follow the log files to see if you notice any relevant message.
Hope this helps.
Best regards,
Cosmin