I can answer a few of your questions:
You can camp at Polentswa with one vehicle, but you will not be able to do the Polentswa Trail.
You can not book for Botswana on-line via SANParks or through their website either. Only way is phone and email request to the Gaborone office.
Gaborone Reservations Office
PO Box 131
Tel: (+267) 3180774 or 3971405
Fax: (+267) 3180775 / 393 2205 / 3912354
Your order of booking will be fine, but include another stop at Mata-Mata when exiting back to Namibia. I won't recommend exiting KTP through Botswana, because if you do get stuck you may not find help quickly and can easily wait for days before help arrives.
When you enter the park through Namibia you still remain technically in Namibia and the only passport control is at Twee Rivieren to exit to RSA or Botswana. My understanding is that you won't be required to get your passport stamp there if you are returning to Namibia, but I have only exit at Twee-rivieren after entering at Mata-Mata and not 100 % sure.
Although you will be in Botswana when staying over at Polentswa campsite it is not seen as exiting the park and no passport stamp required to get to Polentswa campsite. If you however want to exit at Kaa gate you need to declare your arrival into Botswana at Twee-rivieren or you will be send back from Kaa gate to get your documents done.
Are you still a South-African passport holder or do you have a passport from a different country? I am not sure about Visa and what is the requirements for your country when arriving in Namibia. South Africans do not require a Visa and only passport valid for 6 months after arrival date. If you have any children in your party you will need an unabridged birth certificate that stipulates the parents ID numbers for each child plus passports. This is a new rule that will be introduce in Sept / October this year by RSA HA.
The shortest route from Namibia into KTP is via Mata-Mata unless you are visiting the southern part and you want to remain on tar roads you can enter at Ariamvlei/Nakop. This route will require border crossing into RSA with the full cost of 3rd party and road funds. You might not be require to pay it when entering and exiting at Mata-Mata and only if you exit KTP through Kaa gate, Mabua or TR.
I am also planning a trip to Namibia in 2016, but may take the Botswana route from SA and back. You can PM me if you would like to share your plans on the Namibia trip and any question related to Namibia. I've been there 5 times already, but one can always learn about a few new places and tips, because nothing stay unchanged in this world.