You believe that Jira has "encoded" that culture in your company, not that your company has encoded it's crappy culture in your Jira implementation? Please see: https://en.wikipedia.org/wiki/Conway's_law
I saw how that culture evolved over time as the company got bigger. It didn't start out that way. JIRA was once a bug tracker for us. It became a some sort of flowchart madhouse with horrifically convoluted processes around it. Partly yes, because the company felt a need to hire project managers, and partly because the tool existed and therefore there was something for them to fiddle with all day. If they didn't have the tools to create over-engineered processes, it would be less likely to occur.
At some level, yes, JIRA just enables problems, it doesn't directly create them. On another level, its whole structure encourages that way of thinking.
