It is interesting. These highly stunted Shore pines come from only one location, and much of the stunting is thought to be due to the highly hostile soil at that particular location. When collected, as much of the root ball is collected with them as is practical, along with the attached "toxic" soil. I believe the ones collected the longest ago by Dan Robinson have been in captivity now for only about six years or so, IIRC, and he doesn't remove the soil typically. One that I got from him a few years back was from one of his early collecting trips to that place, so also about six years in captivity, I think. Like him, I also did not remove much soil when I potted it up two years ago. He pots his into a 50/50 mix, while I use pure inorganics. We have some minor differences in our fertilizing, watering and placement regimens, but they are not drastically different. And yet, the foliage on the newly collected trees, and both his and my potted trees all look the same length and with the same unusually brilliant and deep green color (maybe very slightly more yellow in the wild). Perhaps the remaining "toxic" soil continues to exert an influence on the needle length even though they have put out new roots into the better soils now. But arguing against that is the fact that other Shore pines, and their brothers the Lodgepole and the Murayana, also have short needles that don't seem to change much with "better" treatment in captivity, although the regular Shore pines and the Lodgepoles have slightly longer needles to begin with. Interesting, I agree.
I think we all have the same experience you do with Ponderosas, although I believe Walter Pall has written someplace about methods to shorten their needles almost to JBP standards in captivity.