I wrote this up this long missive earlier this evening and couldn't decide to post it or not, and it's probably beating a dead horse since John talks about some of this stuff on the LOJ glossary page, but what the heck.
Aside from the listing issues John mentions, there are flaws in the technical analysis. First, using a variety of techniques creates inconsistencies between different peaks and it also implies spurious precision that does not exist. I.e., I don't think you can trust consumer-grade GPS or altimeters or DEM data to better than 20 feet on some sort of 100% basis. (He admits this for the DEM data, while somewhat glossing over the fact that his standard deviation of "only" 5 meters really isn't so great.)
Second, raw altimeter deltas are only a lower bound to the actual delta due to the way most altimeters work and the way the atmosphere works. I.e., unless you are climbing in winter, you will be climbing most high peaks in the lower 48 in warmer conditions than the Standard Atmosphere (which has 8 degrees Fahrenheit at 14,500 feet) and that's the basis for most or all digital altimeters. In particular, the quoted 276-foot saddle depth for Muir could in fact need to be corrected to 300 feet on a warm day (and their measurements were made in July). That's an 8.7% boost and I have measured an effect nearly that large on Colorado 13ers before and I see this a lot in Arizona on warm, quick, medium elevation peaks where there isn't time for significant weather changes. (I have an essay on this technique at:
http://www.eskimo.com/~rachford/mountaineering/essays/altimeter_corr.html)
This technique isn't perfect, but raw altimeter differences during summer are virtually always going to be short.
This is all a long-winded way of agreeing with what John says here and in his glossary page. Although it may not provide a perfect list of peaks, what I like about the LOJ lists is that they are based on a single source and do not depend on any extraneous behind-the-scenes analysis. If one has any doubts, they should be climbing the soft rank peaks to be sure.