Kirk,
HDR is quite a common technique to shoot but is a nightmare in terms of time to sort. But from the data files, it isn't difficult to identify the photos shot with different exposures. For example, shots done through auto exposure bracketing could be identified through coding and if this built in the form of automation, it becomes a huge benefit to sort photos and save HDR workflow separately.
Focus staking is lot more difficult to identify but I would find it helpful to be able to save the images shot for focus staking in a separate folder for processing. Hope this helps.
Vignesh