As I follow the conversation it seems that Nayden got little confused. Your suggestion is really nice. Right now we have only settings per connection not per solution. We're planning to make some changes on the connection settings window and may be if you are able to group your connections you will be able to manage this better. What do you think of that?
I logged a Feature request directly to the Thunder Development team. They will have in mind your suggestion when they consider new functionality to be developed.
Thank you once again for sharing with us this idea!