So to use the rebuld command to clean up seams in surfaces like this, before you use thos top cutting curves, select them and hit the tab key then type Rebuild.. Select refit and delete original, with a tolerance of soemthing like .001.. Then when you extrude your surface, it will be clean and the next cutter will prodice a single cut that should then fillet ok...

BTW, in your original surface, there is a downward "dimple" in the center.. Maybe if you recreate this, you would want a tangent curvature? FYI