Well, as one says “this is not a bug, this is a feature !!” 
Having said so, this creates undesirable side effects:
(a) some eggfile are getting very large with this extra dummy vertices…
(b) more seriously, trying to postprocess eggfile vertices is a headacke since additional or duplicated vertices are bringing confusion.
consider for instance a obj file with 2 faces, 4 vertices where faces are defined as:
f 1/1/1 2/2/2 3/3/3
f 1/2/1 2/3/1 4/3/2
after obj2egg convertion, trying to add a specific property to each original vertex (for various purpose see for instance [Dynamic Composite Mesh - Real time blendshaping)) is really a pain in the neck !!
PS. ok, I’ll try to use egg-trans -c after obj2egg, just hoping that the vertices numbering is back to the original… I cross my fingers