Stencils don’t have anything to do with extracting directly. Extractions are made from a mask, from hidden geometry, or from a layer.
You can bypass the stencil, and apply the alpha directly as a mask. Select a “Drag Rect” stroke type for the Standard brush, select the Alpha you want, hold down CTRL, then drag out the mask shape where you want on the model.
Alternately, you could derive the mask from a texture. (You’ll need UVs for this). Apply a texture or generate one from polypaint, and explore the “mask by” commands in the Masking palette. Use the stencil to paint the texture.
There are probably about a half dozen other variations you could also use to do this…Zbrush provides a wealth of options for working conversions between masks, alphas, and textures.