I just had my wiring harness recall done a few weeks back. No problems whatsoever, even with the aftermarket stereo setup.
However, unlike most other aftermarket radio gear, my Blaupunkt Nevada unit (self-installed) has the standard four holes in the face of the deck a la stock Ford unit and many other European cars (such as VW, Audi, etc.) to allow removal using the Ford factory tool or equivalent.
Also, all of the wiring is done using adapters (nothing hardwired a.k.a. soldered) so that everything can be removed in a snap using factory procedures and all factory wiring connectors and harnesses remain untouched.
Maybe that makes a difference.