I'm surprised they used Bootstrap. Atlassian is big enough to create their own CSS custom framework.
In my view the question is "why shouldn't they build on top of an existing stable base?".
If I made that decision for a business, we would have started the discussion there. An argument for creating our own framework would need to convince me of its value to the business. Just because the company has resources to do it, doesn't mean it is the best use of those resources l.
I can't imagine any company wanting a distinctive design for their components using it.