Hi - Namibia isn't the problem for customs, it's South Africa - but it also depends on the range you can fly with you AC.
Officially you have to use the Keetmans-Upington Route. If you get a clearance for Oranjemund you can do immigration there and fly to Upington or Cape Town.
Alexbay ist NOT an option - I've tried getting special permission, but they would noy grant-it is no longer an Immigration facility. I had to cancel my flight back then. Would be so practical for light aircraft, because they have Avgas.
Remember, there is no Avgas at Keetmans nor Oranjemund. Only place that sells South is Luederitz.