Just a quick follow-up on this post that others might find useful:
As far as I can tell, there is only one scriptable load option currently available in the HDF5 Plugin that is available on the Fiji update site. This means, for example, that you will be unable to load images in HDF5 files with custom data layouts through a macro.
I wanted exactly the ability to load datasets with custom layouts without resorting to the GUI. I therefore slightly modified the HDF5 Plugin to expose the load functionality for custom data layouts to a scriptable interface. The modified code may be found here:
I hope this helps others who are looking for similar functionality.