お客様は神様です "The Customer is God"

I came across an article in the Japan Times today entitled, "In Japan, the customer is not king." I usually try to stay out of discussions like these since they have a tendency to turn into flame wars, but after reading the article and the responses to it, I was compelled to offer my response, which I included below. Here is a link to the original article; my response follows.

I hope folks won't mind if I play devil's advocate here. My comments are not directed at any of the responses, nor are they meant to imply that anyone is wrong or insensitive. I merely want to offer a different point of view.
I haven't yet had the experience of being a resident in Japan, but I have spent quite a bit of time there. Furthermore, as someone who works for an international company that does business with big companies in Japan (both the modern and the antiquated ones), I think it might be a mistake, categorically, to draw inferences about Japan's ability to compete in international business based on the experiences of customers in Japanese shops and restaurants. Since this article is primarily focused on the experiences of the latter, I'd like to focus on that.
I know people are fond of the 客様は神様　"Customer is God" proverb、but it's important to remember that there are other factors at work in everyday Japanese consciousness that work in the opposite direction, as well.
I'm reminded of a passage in a novel by 向田邦子 (Mukōda Kuniko) in which the author observed a group of western ladies ordering breakfast at a hotel. She was very surprised that the ladies were so incredibly particular about the way they wanted their meals prepared. She reflected on the example her mother had set for her as a child, and on the idea of having compassion for the wait staff and the chef and cooks who will prepare the meals. She concluded that it's better to stick to the menu and keep it simple when it's tolerable to do so. Here, it might be suggested that the concept of "Customer is God" may include the supreme compassion of a god (lowercase 'g'), and not just the omnipotence of one. Now, Mukōda-san was a Showa era writer, of course, and we might conclude that things are or should be different in modern Japan. With this thought in mind, however, it may be more than just a coincidence (and more than just mere complacency) that "The common (Japanese) man or woman on the street generally accepts the way things are delivered in their vanilla form," no?
The examples given in the article appear quite extreme, so if I may, I'd like to relay an equally extreme experience I had not that long ago. My wife and I were waiting for our waitress at a restaurant in our neighbourhood in Chicago. The waitress was busy with a customer at the next table who was asking to have one of her ordered items substituted for something else. She then started asking about what kind of bread they have and if she could have a bagel instead of the choices she was provided. When the answer was affirmative, she went on to request that the bagel be split in half, lightly toasted and that the center be pulled out. I couldn't help but think, "What the hell?" Maybe this is supposed to be OK, I'm not sure. It seemed really extreme to me and bordered on rude considering the tone she used when speaking to the waitress. Regarding the experiences such as the beer with no foam, couldn't it be that the measurement of portion size in Japan is all about the volume/quantity and not the size of the container as it seems to be in the West?
Anyway, no conclusions here-- like I said, I just wanted to offer a different perspective. I would like to end by wondering something, however. If we are to expect of Japanese customer service the same standards we've become used to in the West, are we perhaps trying to inject a sense of western individualism into a society that basically operates just fine without it?