Cost Center Management on Position level vs. Department Level

Hi everyone.

My workplace is currently implementing the financial module in a pre-implemented HCM environment.

We are having hard time to understand the best practice of cost center management in an implemented HR department tree.
Like many organizations, our HR tree and cost centre tree are not the same.
Sometimes the HR tree requires more granularity in department level and sometimes the cost center tree does.

We were told that the only way to implement the cost centers would be on department level, but this will require HR tree, in some cases, to be more granular than required. For example employees whose cost is different but report to the same manager will have two different departments!