The usefulness of the HDR tool is a little questionable. Bracketing for HDR exposure is feature of the camera, with plenty of user choices including number of exposures as well as the how far to increment the exposures.
But I'm wondering if the manual is a misprint, because I just tested the HDR tool, and it varies the exposure time, not the aperture in capturing the sequence.
All the tool does over the normal bracketing method is add some metadata which can be read/used by C1. But since C1 doesn't actually merge the files I'm not sure how useful that is. (maybe a future feature?)
The HDR tool uses whatever is in the bracket settings regarding number of exposures and variation. so you can't use it to have a "second" set of settings quickly accessible.
As an aside, I couldn't get the camera to vary the aperture during any bracket sequence ... Using TV, AF, P or manual all resulted in the camera changing exposure times, none of those modes changed the aperture to vary the exposure. This may be different in a situation where there is a lot of light, I just had the camera sitting here in my office testing it.