Reading just above and below the Eng Ref section you quoted, I believe this is saying that this Space Discretization Constant is a global setting which EnergyPlus uses to calculate the number of nodes within each material layer -- you don't have direct control over the number of nodes. See highlighted portions from the Eng Ref section below.

In summary, increasing the Space Discretization constant will reduce the number of nodes for material layers depending upon their thermal diffusivity, thereby reducing simulation time.

It does not look like you can apply Conduction Finite Difference (CondFD) to just one specific material layer within a construction assembly. However, you can apply CondFD to individual surfaces or construction assemblies in multiple ways:

• a specific surface
• a surface type
• a list of surfaces
• a specific construction assembly

The other surfaces and construction assemblies in the model will use the global heat balance algorithm. This may be enough to apply CondFD just to the surfaces with a construction assembly that contains the thinner layer you want to focus on, reducing the simulation time by applying a different heat balance algorithm (likely the default conduction transfer function) to the remaining surfaces.