With the first party isolate, mechanisms such as oAuth would not work. So the containers are less restrictive, but still allow you to have two sites with the same cookie context.
Everything else, including tons of single sign in/OAuth websites, work without any issue.
Unfortunately of course it'll always be a minority, and won't affect whether even those people (have to) use Jira or whatever, so not really any incentive for Atlassian to fix it.