As I have many open tabs already, currently I can not set a container type to be the default to open new tabs in, and containers are supposed to keep cookies separate from other containers, how does the isolation work between tabs I have opened in a container and tabs that are not assigned to a container? Does the isolation still apply?
Yes, the isolation applies - cookies are isolated between each container AND between the default userContextId (which is 0).
What I personally did was to sign out of all my websites/accounts in the default, non-container context.
There’s a very popular issue open to assign certain sites to always open in certain containers: