I wish to get a clarification about the $ 20 or $50 we normally pay to temporarily drive a foreign car to kenya.foreign permit.with the customs union on zero tarrif. How will this be treated?

When it comes to taxes the Customs Union is only concerned with EAC tariff that is import duty which is zero for goods traded between EAC Partner States. Another EAC tariff is Common External Tariff (CET) for goods coming outside EAC region.

Other taxes are domestic taxes and don’t fall under EAC tariff so each country will continue to charge its own taxes (domestic taxes) as per national laws. The charge you are talking about is a domestic tax. It is until EAC Partner States harmonise domestic that such incidental charges will be dealth with.