Ken Jones just made an interesting post on cohp.org
In specific, his post notes that while the benchmark elevations of Colorado 14ers Eolus and Windom are at 14083 and 14082 feet respectively, neither BM is on the summit. When the USGS did their survey, they kept notes that the summits of the peaks were 1 and 5 feet above the BM's. This makes Eolus 14084 and Windom 14087. Thus, Windom is the actual La Plata County highpoint.
In general, one might wonder what the average error is when using BM elevation as a stand-in for summit elevation. Ken had to specifically request his info from the USGS, so presumably it would be a tedious task to correct the data for thousands of peaks.
While probably this is not a huge issue overall for the lists, some effects might include changes to highpoint lists or peaks getting a few more feet of elevation and prominence. For example, is "Iroquois", Colorado really ranked? Presumably the BM is not up on the precipitous boulder-top.