I wish I could give you better answers, but I don't even understand some of the questions or terms like cross-tracked. I can only say that from one workspace that contains a Vivaldi instance to another that contains a different Vivaldi instance, I've never seen any interference from one to the other.
I do believe that the settings are common, but I've never researched that.
To the best of my knowledge any Browser shares cookies regardless of whether you have one instance or multiple instances of it open.
brent if you wanted to use Vivaldi to have different sets of Cookies you could do that. You would use their Profile Management options to create a new User Profile. This functions very much like Chrome's multi-user profiles but from what I know Vivaldi developed their profiles and sync separately from Chrom/ium. They have a strong privacy stance and I would think this would be the way to go.