The point is that there are direct taxes and indirect taxes. Direct taxes are apportioned as you say. Indirect taxes do not need to be apportioned.
You seem to be confused in that you seem to want to apply the rule on direct taxes to indirect taxes. The 16th Amendment was passed so taxes on income from property would be treated as an indirect tax. Income from wages, excise taxes, tariff, and various fines and fees are indirect taxes.
Taxes on property as property, or on a per head basis would be direct taxes, and would still be subject to apportionment.
JWK