I haven't seen that issue, but my use cases are pretty simple:

When I need to open a GitHub tab for my organization admin account, I open a new tab in my "work/admin" container first, then nav to GitHub. Child tabs are opened in the same container. This is 99% of my usage.

Following an incidental link from elsewhere to GitHub will open in the default account/primary container (or "no container"). Or, you can right-click and select "Open in New Container Tab > Container X" if you are aware of the need to switch accounts ahead of time...(and if you are not, there's "Reopen in Container > Container X").

I don't use the multiple-windows/multiple-containers model. There might be an extension for "open all tabs in this window in container X" though.

I use Profiles and multiple windows when the separation is important, and Containers in the same window when the separation is merely convenient.

one problem for me is opening links from the outside, like from emails, into the right container. there is no UI to choose the container before the link is opened.

this is also a problem with using multiple profiles in different windows