Not in the way you're hoping for.
If you follow the standard "here's how to install Jira and Confluence" documentation, you will end up with systems that work fine. They do assume a basic level of knowledge about the Operating System and Databases you are going to be using, and they make a handful of specific "if you are doing X with this config, then you need to do Y to make it work well".
But beyond that, if you've got config, tweaks, libraries or whatever that are not off-the-shelf, then you've done them for your own reasons, which we can't help you with.
Classic example - I built a test system on three RHEL 6 servers I'd been handed by our infrastructure team. I used our internal RPMs to install Java and the database server, then did Jira and Confluence as per installation docs. This all works absolutely fine.
But, when translated to live, the database needs some tweaks to enable the correct replication for backup, there's some SSL related tweaks as it's (sort of) public, some rsync and more database settings for failover/disaster-recovery. But all of those changes are because *we* need to do *our* things in *our* way. There is a good chance that some or all of them are utterly useless for other sites.
So, I'm afraid the answer to "why was our server set up this way" is "if it differs from the Atlassian documented setup, then it was done for your reasons and we can't possibly know why".
If I was in your position, I'd try building a test system from the docs, from scratch. Then compare all the differences with Live and investigate them.
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