there's different installation processes for each product, some are very similar, others not so
the admin web control panels can also be very different, making it hard to find equivalent settings in different products
when you're looking for log and configuration files, they're not necessarily where you expect them to be
I suspect part of the problem is that some products are from a forked common code base which diverged, and the others which were not Atlassian products originally are skinned to look like them, and there's some attempt to make their code base converge with the others.
They are totally separate code bases that have similar choices as far as aesthetics and design decisions. Some features they add today may start in a similar code-base but they are often purpose built for each application. They are unifying the user interface where possibly by setting standards and libraries.
I doubt they will see much more unification than UI.
There's been some convergence over the years, but I do feel that it's been weaker than it could have been. @Paul Mansfield mentions one point that is spot-on - the "logging and profiling" admin section in JIRA is really helpful, and in the other products... well, rubbish. It should be the same in all of them.
The æsthetics have definitely converged, which does push the product owners together, but it still stands improvements.
And then Paul also makes another good point about the history - Atlassian was founded on JIRA and after a few years, Confluence arrived. But a lot of it is acquisitions that gradually get merged in properly. For example, JIRA Software still has a pile of references to "Greenhopper" in it. (No, not Grasshopper, please remember that spell-chequers are dumb). Clover, Fisheye, Portfolio, etc - acquired and gradually moved towards Atlassian standards. Even Service Desk and the UPM are based on non-Atlassian stuff.
But. The products are different. I'd like to see them work the same on common principles - clicking "admin" and then going to logging, user maintenance, email servers, file storage, etc should look exactly the same across products. But 95% of the admin items in JIRA don't translate to the other products and hence have different interface requirements. And 95% of the admin of Bitbucket systems don't apply to the other products... etc
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