Pretty sure you cannot have different heirarchies in the same Jira instance. Multiple Jira instances could solve that problem. Another way is to setup the heirarchies by mapping them to issue types, but then don't put all of the mapped issue types into the project. This doesn't change the hierarchy structure, but the teams who don't need the extra issue types will be blocked from creating them by Portfolio. Not elegant, but allows for some differences in hierarchy use.