Hierarchical data in ETL

I'm new to ETL tool, but what I find out evaluation them that they all work with flat row model. I.e. if your data requires some graph object transformation (i.e. checking parent fields or other dependedcy) it is very inconvenient(it is solvable with denormalization etc for mapping to simpler RDB model). I want to ask whether I understood it correctly. And why ETL avoid working with more understandable to the business object oriented models. Is there are ETL which support Document related, or OOP related transformation?