The second part discusses in more detail the actual role played by holonomy perturbations in the proofs.
In fact, the holonomy-perturbed flat connections interfere with the representation variety of the knot
complement, and in a more flexible way than one may have thought. The essential non-triviality results
for the space of these perturbed connections come from the TQFT-properties of instanton gauge theory,
and from a theorem of Kronheimer-Mrowka that states that the 0-surgery on a knot embeds as a splitting
hypersurface in a symplectic 4-manifold whose Donaldson invariants are non-trivial.
Links:
[1] https://www.mpim-bonn.mpg.de/de/taxonomy/term/39
[2] https://www.mpim-bonn.mpg.de/de/node/4234
[3] https://www.mpim-bonn.mpg.de/de/node/7451