Most of today's modern engines use a concept called "valve overlap", the period when both valves are open near TDC. So on your engine your assumption of valves closed at TDC may not be correct.
Are you looking only at the cam gear or do you have the crank gear exposed also? The crank gear will have reference marks as well. Some older Hondas had a mark on the crank gear that had to align with a mark on the engine case. Once the crank is set, then move to the cam gear indicator. On new Honda CRF's, the dot on the cam gear has to be in parallel with the head gasket surface so in this case there's no reference point on the case. You almost have to be overlooking something. Think about an engine in a production environment. If the setup were left in the hands of the assembly worker and the process was this mysterious the manufacturers would never meet production.