Would be great if you could choose which layers to include in the resulting layered pdf tree.
When printing to Pdf using EngageBatchPrinting the layered Pdf tree shows the Temp Map Mask layers which are generated when batch printing,
Given that these are not needing to be shown in the resulting Layered PDF Layer Tree (only in the map)
you should have the option of which layers to include in the tree.
The image also illustrates the layered pdf nesting issue that exists when concatenating pdf maps using batch printing which is noted in another post.