I see you posted this several months ago, but I'm just now seeing it. (Sorry!) The first trip you mentioned, the storm is a lot of driving, long distances in a short amount of time. It's doable but you'll see more of the country from the car trying to make kilometers than spending time at your destinations.
The second option is better, however Rehoboth and Waterburg are odd additions when there could be more time added somewhere else.
Most of the trips that I fly for people have two nights Sossusvlei, two nights Swakopmund, three nights Etosha and occasionally one-two nights in the Twyfelfontein area. I find that putting Swakopmund in the middle is a nice break in a smallish town before heading back out into the bush for 5-7 days.

What time of year are you looking at doing this? I can put you in contact with some of my travel agent friends here who I know personally and have used personally for my own travels, they may be able to get you some other really nice itinerary options.