This question is in reference to Atlassian Documentation: Understanding stages and skills
The JIRA Portfolio adds the concept of percentages for the stages and skills, but the documentation doesn't explain how this impacts planning. I also see that for issues I can specify specific skills, but when doing that I will assign either story points or days/hours. So, why the percentages?
A suggestion is to customize the time allocated to that skill that is either not needed or doesn't need to be what % is defaulted to. In the Scope listing, add the Estimates column to the list. Then modify the allocations manually in the list. In this way I have been able to set a given skill to 0 and remove those errors if that skill is not needed.
PS, the percentages are used as a default setting to break the estimate up across the skills. As I mentioned above, you can manipulate those values manually by changing them in the estimate field in the scope listing. (Assuming Portfolio 2.0)