Good Customer Service - customer no longer always right?

I'm sure it wasn't that long ago that companies treated customers with respect - and went by the saying "The Customer is Always Right". 

Well it doesn't seem that this is the case any more after a few different retail experiences - I can see why people are starting to do everything online if they are anything to go by.

My most recent "poor" experience is with one of the largest technology companies on the high street. Apple.

I purchased a high end (as in top of the line but one) Macbook Pro Retina 15 online. And had the machine for a week. All was well.
Then it developed a hardware fault. After discussing it with a technical support representative, it was decided that the best course of action was to swap the machine in-store due to the fact it was so new, developed a fault, and that returning it via courier was going to be awkward (my current situation with my son means I'm not home much ... and never during the week at working hours!). And so a 110 mile round trip the Apple store began.
The Apple store in question, Newcastle Metro Centre, didn't have my exact model in stock - but had the marginally newer one, with its grand total of 0.1Ghz faster CPU.
But because I had purchase the machine online they were unable to swap it for this newer SKU. Nor were they able to take it in to return it to Apple for repair on my behalf. All they could do was to "attempt to repair it in-store". Note the word attempt in there. Not overly spectacular considering the cost of the machine in the first place, nor what the technical support rep said, or the fact that Apple seem to make a deal of saying they offer "excellent customer service". Perhaps they do, if you purchase in store - it seems that if this had been the case the machine would have been swapped no questions asked. 

So how do Apple justify this difference between in store and online? They trade as different companies. One for Apple Retail, and one for Apple online - so why do they get away with trading under the same brand? It all seems like it is intended to just confuse members of the public, and I have to admit I did find it confusing - they are the first company that I've come across that have this disparate split between online vs retail.