By segregating as much as you can. Definitely not by putting everything in a single table. At the very least separate databases/schemas with proper permissions so there's not any chance of data intermiBy segregating as much as you can. Definitely not by putting everything in a single table. At the very least separate databases/schemas with proper permissions so there's no chance of data intermixing.
The best would be multiple separate database instances, which is not even hard to manage specially for qualified engineers like Atlassian surely has plenty of. The problem are business decisions of ignoring the tech debt, usually...
Now every time you run a database migration, you have to adjust N tables - and in Atlassian's case, N is 200000. Is that better? It depends. There is no "best" way of doing multitenancy.
The best would be multiple separate database instances, which is not even hard to manage specially for qualified engineers like Atlassian surely has plenty of. The problem are business decisions of ignoring the tech debt, usually...