Why aren't the bonus skill points being added?

It doesn't quite work that way. The bonus is added to the creatures that are higher in the hierarchy. If it's based on the army's experience, then it applies to them; if it's based on the creature specialist, then it applies to that specialist. But not both at the same time. There's nothing that can be done about this because the modding community is more interested in the visual appearance of various things, animations, and other insignificant stuff that doesn't really add much value, like last year's snow. Unfortunately, no one wants to focus on improving the Heroes of Might and Magic options, refining the gameplay balance based on the realities of Heroes of Might and Magic, and removing the idiotic quantitative limitations of the original game in both the game and the map editor.