We don't have a solution for non-cloud org level shared protos currently, see TypesProto for merchant/reports API and TypesProto for merchant/inventories API that generated duplicated classes for the same shared protos.
In short term, we would need to manually create a new module for these common protos for shopping org and set up automations to automatically update the module if there is any changes to the protos, or add them to java-common-protos.
In long term, we need to have a defined process for these non-cloud org level shared protos in case it happens to other orgs.