I have had several clients go through this process in Frankfurt with Delta/Air Namibia flights all issued on one ticket. Most have obtained the permit in advance because they ended up with an overnight Frankfurt on the return due to an Air Namibia schedule change. I'm not sure that any of them actually wired the money for the permit. The reports back so far are that they were able to get Air Namibia in Windhoek to check their bags all the way home even though they did overnight in Frankfurt - the bags remained in transit in the airport. No questions, no problems in Frankfurt and never asked to produce their permit or proof of payment.
I think the key is for the bags to be checked through to your final destination and not have to claim them in Frankfurt. Be careful as not all airlines have a baggage agreement if you are flying Air Namibia and have a separate ticket on another airline.