Poor Planet X setup

I read in a few places about people having to disassemble and re-grease their PX headsets to keep them quiet. I know I did.

This isn't high end engineering. It's dead simple, and takes 1 (at most 2) allen keys and some grease. You should be doing this yourself.

I ordered a bunch of parts the other month under the assumption that it would be next day delivery, because that's what their website said.

Next day, nothing. Day after? Nothing. Day after that? Still nowt.

Eventually I emailed them and asked where my order was and got the answer:

"I have contacted our shipping department to see where your order is.

When I have a reply, I will contact you."

I mean, really? Surely it should have been a question of their customer services asking their shipping department what was going on, if it had been shipped then provide me with a tracking number, if it hadn't been shipped find out why and explain it to me.

Eventually I was told the item was on its way to me and got a tracking number off them. When I checked with the courier it was still at Planet X waiting to be collected.

All in all, it was a bit shoddy. If they'd have just said "Look, we're busy, we've made a mistake, we're sorry" I would have been alright about it, but their deliberately vague responses followed by what was essentially lying really soured it for me.

My Planet X came out of the box perfectly set up and adjusted - it is also a fantastic bike.

There isn't really much 'set up' on any groupset, align it, set the upper and lower limits, then take the slack out the cable.

What caused the creak?

You ca. Adjust dérailleurs till the cows come home and say it's 'better' and I have no idea what the 'wrong' lubricant is either, unless it's tallow, just about anything else is personal preference, assuming its proper lube intended for bikes.

Adjustment and lube (in my opinion) is users responsibility to do themselves or have serviced, original shop only sold you the bike, sure, in the good old days when your LBS could charge full RRP they might have cut you some slack, but the margins on new bikes are slim, especially with the likes of PX, Ribble and Canyon.

First let me say that I have bought a few odds and sods from Planet X and I've been satisfied with their service and I reckon their prices are excellent. But I've never bought anything as big, or important, as a bike from them, and I never will.
So why, if they have always treated me well, won't I give them large lumps of cash? It's because my father was right after all. Fifty years of spending his hard-earned money had taught him you get pretty much what you pay for.
There will always be the odd exception of course, sometimes the stars align and everything goes right, including a bargain price. And occasionally, I confess that paying full price leads only to disappointment. But, just like dear old dad, I have mostly found that if you pay bottom dollar you get low level service. And the hassle of being hassled by incompetent mechanics or sales staff is too much to bear.
Buying a bike should be a joyful experience. Doing the research, reading the reviews, finding the retailer, taking advice from wiser heads, immersing yourself in the anticipation, soaking up that first ride, all these things are part of the package. So why put them at risk for the sake of ten percent?

They're really cheap, are Planet X. The bikes and components are generally great, so I guess you've got to accept corners are going to be cut somewhere. Canyon are similar - bikes need a good service from a trusted mechanic fairly soon after buying them, from what friends have told me.
Sucks, but that's life really. I can heartily recommend building a bike yourself and picking up some skills from that. Suddenly those little roadside breakdowns are a lot less scary.

If their customer service is good, go back and make use of it. Let them know that they did a poor job and you had to take the bike to another mechanic to get it properly fixed.

Adjustment of derailleurs doesn't leave much room for personal preference. I'm not sure why that would ever affect chain length but perhaps I misunderstand that part of your comment.

If Planet X did a poor job on the Nanolight, why did you buy another bike from them? It sounds like you might have predicted the service issues with your RT-58 from previous experience. Technical and customer service are what differentiates one dealer from another. The bikes are mostly the same quality at a given price point, so it makes sense to choose a shop primarily based on their service.