I've read the injector harness can cause issues, too, so that would probably be a good thing to check with the engine out. Any remotely suspicious back-of-cylinder head stuff would be far better taken care of pre installation, especially in a longitudinal mounting application.
Having to replace the injector harness on a PD in a longitudinal installation is one of those jobs I (and we all) just hope to never have to do. I know someone who had one done by a local shop with a not particularly exceptional reputation in Livingston on a BHW car, and somehow it didn't cost much, and certainly they did not remove the head or the engine to withdraw the harness and its plastic skeleton. I guess I can only assume they just busted up the plastic structure into pieces and managed to get the wire harness out that way, and then who knows what they did when putting it back in to support the wires. That motor is still on the road now in a swap vehicle, running fine. So whatever they did worked out, at least for now.
Failure of the PD head harness seems uncommon enough that it's hard to see logic in proactively replacing it .... but it'd sure be painful if it needed to be changed not long after an engine went into a swap... Hard call. I don't know how expensive it is either. Bummer they designed it the way they did, you'd think they could have had plenty of other options for how to do it, knowing that the PD was intended for use in lots of longitudinal Audis and Passats.
On the smart actuator (which is just a position sensor piggybacked on what's otherwise a normal vacuum actuator for the BEW, and maybe BRM? can't recall -- but it still runs off vacuum and an N75 for control movement), I don't see why you couldn't just leave it in place and plugged in if your tune is written to ignore it. Or unplug if you're swapping to a different turbo with a dumb actuator, and it'd be the same effect. I can't think of a reason you'd need to remove the actuator position sensor just for the sake of eliminating it, it won't affect anything functionally.