I think you may be referencing the quoted paragraph (pg. 469 - pg. 471). In future: it is helpful to point at specific parts of the reference, since it's possible I'm barking up completely the wrong tree.
Overall, I think the confusion comes from the fact that the author is making claims about particular, (usually) highly symmetric polyhedra. While you seem concerned with whether the mentioned properties apply to all deformations of the particular polyhedra.
For a given geometric polyhedron the construction of a dual polyhedron
is most often carried out by applying to its faces and vertices a
polarity (that is, a reciprocation in a sphere). From properties of
this operation it follows at once that the polar of a given polyhedron
is a realization of the abstract polyhedron dual to the given one.
However, the possibility of carrying out the polarity depends on
choosing a sphere for the inversion in such a way that its center is
not contained in the plane of any face. While this is easy to
accomplish in any case, the resulting shape depends strongly on the
position of that center. The main problem arises in connection with
polyhedra with high symmetry (for example, isogonal or uniform
polyhedra) if it is desired to find a dual with the same degree of
symmetry: If the only position for the center is at the centroid of
the polyhedron, and the polyhedron has some faces that contain the
centroid – then it is not possible to find a polar polyhedron with the
same symmetry.
I suspect is possible to construct a polyhedron with its centroid contained in a face such that there exists no deformation which moves the centroid out of that face (without moving it into another face, at least). Even if this is not the case, the author states that for a polyhedron which has only one valid center of inversion (at the centroid) the polarity is not well defined. Of course we could deform the polyhedron (and lose some of its symmetry) and this may fix the problem, but no claim about the (im)possibility of this is made.
I'm not qualified to say whether such deformations exist, and even my first suspicion is a bit of a stretch. Perhaps another user can add to this.
Moreover, if a polyhedron has coplanar faces
[coinciding vertices] then any polar polyhedron will have coinciding
vertices [coplanar faces]. All these possibilities actually occur for
various interesting polyhedra. Clearly, duality-via-polarity is
uninteresting for subdimensional polyhedra – it yields only trivial
ones.
As well, I don't see a claim that the perturbation you are asking about does not exist, but the claim is that if a polyhedron does indeed have coplanar faces then the corresponding polar polyhedron will have coinciding verticies. This is noteworthy since many highly symmetric polyhedra of interest will have coplanar faces, and thus the polar polyhedron must have coinciding vertices unless we destroy some of the symmetry of the original.