There is only one remoting tag in the config file, so yes, this does mean the client application can talk to only one BOS. We've discussed opening this up for multiple app servers, but this feature hasn't bubbled to the top.
You can, however, set the PersistenceServiceOption argument when you create a PersistenceManager. This defaults to using whatever is specified in the config, but you can override it to specify that the particular PM use only local or only remote data sources. This is primarily useful when you will usually be using a BOS but also need to use a local database.
In your case, if you can always access the main database from the client with a direct 2-tier connection to the database, then maybe the PersistenceServiceOption will work for you. You can contact us directly if you'd like to discuss your options further.