Atlassian would want integration with their backend products to increase lock-in and provide a place where their products are centered. IT control how products are presented to end users in organizations that matter (in terms of sales volume.) Establishing visibility and driving engagement is hard if the Atlassian tools are a niche and they want to attack SharePoint or other products. Being able to more efficiently use the tools the company has bought is attractive (even if not a reality.)
Making their browser incompatible is a bad outcome for them because it's an IT choice to adopt their browser. This carries visibility and risk for IT who could be embarrassed. Any backlash carries over to other Atlassian products or affects renewals.