The iTMS "album-Only" restriction is not, in any example I've seen, based on popularity. It is based on song length. Their deal with the labels stipulates that all songs under a certain length would be $0.99 each, and that songs over that length would be "album only" unless the label makes an exception (which they have, at times, but most often not).
Amazon, most of the time, seems to sell these "double-length" songs at "double-length" prices - $1.29 to $1.49 so far as I've been able to find. Your example is the first too-long song I've seen on Amazon for "regular" price!
You are correct, although I have seen some songs going for $1.94 on Amazon as well. 3 of them are on Pink Floyd's Wish You Were Here album. One of those songs isn't even that long, like 7 and a half minutes. The other two are over 12 minutes long so it's understandable. I guess for "American Pie," it's such a popular song that they realized people would not want to pay such a high price for it and that they were better off charging a lower price in order to get higher sales.
The only thing which has brought lower consumer prices on music in the past 20 years has been Apple's entry into the digital download business.
From what I can tell, even that has not helped much. We're still getting ripped off for the physical product and in many cases, the iTunes version is an even bigger ripoff than the physical product. The music industry is certainly in a free fall right now, and a big reason is because consumers finally have the choice to download a hit song from iTunes, other legal stores, or illegally. People aren't being forced to buy whole albums just to get one song. Prices are still ridiculous though and eventually they will realize that even with inflation, they are overcharging the consumer versus the 1960's and 1970's when there was a boom going on. They also need to realize that putting out good music will cause sales to go up. The labels are like Hollywood right now: out of ideas and out of creativity, at least as far as mainstream artists are concerned.