I didn't notice it before. When resetting a hero with level 5, 10, etc., the skill tree seems to change. Now, at level 4, no magic skills were offered.
I checked – it's true. A school skill is not offered at level 4. Wisdom is not always offered at level 6, but it is offered in 100% of cases at level 12.
In any case, I don't know of any standard tools to eliminate this effect. It would require digging into the executable file. Although, such a tool would be useful for synchronizing the skill tree on a mirror server with identical heroes.