All hubs share the same connection object therefore they all share the same configuration.
If you want to have 1 server but multiple connection configurations for hubs you can do the following:
app.MapHubs(yourPathToConnectionWithConfigurationA, new HubConfiguration
{
Resolver = MyResolverWithConfigurationA
});
app.MapHubs(yourPathToConnectionWithConfigurationB, new HubConfiguration
{
Resolver = MyResolverWithConfigurationB
});
Therefore when you want to use configuration A you connect to that server end point and when you want to connect to endpoint B you connect to that endpoint. Keep in mind the hubs will not share clients/connections across the two configurations even though the hubs will be on both.