That's because the deformation occurs in the assembly part itself rather than the component. Open the Part Navigator with the Assembly as the Work Part and you'll see the deformation feature. If deforming a part caused the deformation in the component it would affect all instances of that component. But you can deform each instance, individually of a deformable part, within a given assembly.
ER 1329688 - Allow deformable parts to be promoted or WAVE linked in assemblies.
For what purpose do you need to WAVE link the geometry? I confirmed that it's not possible, and it appears that you might have to Extract the geometry into the assembly level in order to change it. For example, I had to use "Menu > Insert > Associative Copy > Extract Geometry" to extract a body before I could use any Synchronous commands on it.