You miss the point Juraikken. The examples discussed demonstrate why we will see in the fossil record is only divergences that are most often well above the species level.
We see in the fossil record differences develop over time that are clear and if we were categorizing today we'd be at the family or order level because they are big enough to show up in the bones.
However, we can be fooled the other way when there is a wide sexual dimporphism and we might thing male and female are different species.
your example had an observer, we cannot observe the past because we were not there.
A very common misunderstanding this is. We very, very often observe things in the past. "Observing" isn't just looking at something it is also seeing the effects it has (an aside -- we never actually observe a n y t h i n g right now-- we see light from it a tiny bit later than it's 'now' but that is a silly detail).
We "observe" that a building existed of a certain size by finding foundtions under the earth. We can observe a number of things about this building without seeing it standing.
If we see hardened rock of a certain kind and form we "observe" that lava flowed under water.