I would guess that the hierarchy is based on the order that the features are written. So to change the order, you will need to sort all your features before they're written

You can set the layer order on the feature type level, higher numbers are drawn later:

Documentation: https://docs.safe.com/fme/html/FME_Desktop_Documentation/FME_ReadersWriters/pdf2d/feature-type-param-w.htm

You can also set the feature order within the same layer (feature type) by setting the format attribute "pdf_feature_order", see https://docs.safe.com/fme/html/FME_Desktop_Documentation/FME_ReadersWriters/pdf2d/Feature_Representation.htm

My apologies for not providing enough information in the original question. When I use the word hierarchy I am referring not just to layer order, but to having multiple parent "folders" in the list of PDF layers.

I pulled the following image from a GIS Stack Exchange post with a similar issue:

Right now with FME all the layers I can create fall under a single "Layers" folder. I am curious if it is possible to create layers under multiple folders with different names - one parent folder for Landbase, one parent folder for Utilities, etc.