It’s a nightmare to use system generated GUIDs in dependent objects. In addition, it doesn’t support ability to provide custom object ids (GUIDs) for some objects (for example for Departments).
You simply need to review documentation once more and choose right tool for your tasks. Yes it is a complicated tool, but at the same time it’s very powerful and flexible tool. I saw a lot of messages from customers and partners which say that FBL is very complicated and difficult in use. Today I am going to tell about Fusion HCM File-Based Loader(FBL) and Spreadsheet Loader(SL). I gained some practical experience and I’d like to share information about it with you. During the last month I had a deep dive into Fusion HCM Bulk Loading Tools.