I agree that your proposals under #1 and #2 do make sense and they are already in our internal team portal for further discussions within our team which would lead to a decision if the default behavior will be changed or not. The current default behavior is based on certain decision which were made because of some restrictions in the first versions of the Visual Designer, but they will be re-discussed following your request. At the moment, none of the current default behaviors can't be changed/configured with the actual version that you have installed at the moment.
As for request #3, this is something i am afraid can't be changed at this stage. The reason for this is the fact that the Visual Designer requires a connection string during design-time in order to have access to the database. That connection string must be in the same project as the .rlinq file as it is not so straight-forward to traverse the whole solution for connection strings during design time. During runtime however, you can remove all configuration file which you feel unnecessary and leave only one connection string in your actual executing project, a Web or Win Forms/WPF application.
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