The short answer is that the allocation method in the Skills Analysis module is different from the optimization calculation method used elsewhere - by design. The Skills Analysis method provides a slightly less precise analysis with more precise node rollup options than are available with the Optimization options. The allocation method in the Skills Analysis module makes no distinction between resource and skill assignments. It summarizes all demand by Required Skill on Effort Forecasts. If a resource has an assignment with no Required Skill, that demand is summarized to a “skill” called “Resource-No Skill”.
The allocation method triggered by the PDWare optimization commands allocates ALL named resource assignments first and then uses any remaining unused capacity to satisfy shortfall as specified, either just on skill assignments or on skill assignments and on resource assignments with shortfall.
See the article about optimization options for more detail.