Thanks @keflavich. I saw the hdu option, but hoped to find something to plot all the extensions in the same image easily. My source/photometry/ds9 region files are all on the extension level, so I tried to avoid the ugly hack to make a single extension mosaic and rerun stuff.
@taldcroft - I have a question regarding table hstack/vstack. Is there a way to keep all conflicting metadata when stacking tables? (e.g. it can be useful having an option to keep the conflicts with a suffix similarly to the conflicting column names with table_names)