Using Autorig and clicking the “Operator” option and select my FBX already loaded into the scene the rig is created and the mesh does not deform.

if I select “file” with all the same options and load the same FBX I get a Rig that deforms but all the materials are stripped? ( has 5 materials ) materials are not even listed as groups after rigging.

I have the "capture|Deform by Default turn ON is all cases.

Without seeing the FBX it's hard to say what might be going one
the Operator option simply points to an operator in your scene and feeds that path to an object merge inside the stand_in object