Other than engine and transmission, are there other parts of the car that are considered in order for it to be "numbers matching"?

There is no standard definition that I have ever seen.

Personally, at a minimum, the power train (engine, trans, axle/dif.) should be original, with all VIN (ex '67), part numbers, and serial numbers as built and match the body numbers. I'm also more strict and believe the major components of the engine; heads, manifolds, carb, air cleaner housing, valve covers, etc. should look original with correct part numbers if possible.

I would personally call a car with a replaced major power train component with the same part as used by the factory, "numbers correct" but not truly numbers matching.