The problem is how to interpret §41. In general this paragraph means that citizens of the mentioned countries can apply for a resident permit / long term visa AFTER they entered Germany under the visa waiver (90 days rule). Everybody else must do this BEFORE entering Germany. The question is now if this also applies when you already are in Germany and have applied for your resident permit and you are waiting for it. Only a lawyer can give you some more concrete advise.

For example when you wait for a green card an you are already in the US with a visa you are normally not allowed to leave the country. You need a special permit to leave and re-enter. Sounds to me that the German rule is similar.