The following response comes from EPE after speaking with Billboard Magazine:
"The confusion seems to come from the fact that these stats in the article are ONLY based on the Billboard Hot 100 chart, which launched in 1958, after Elvis’ landmark years of 1956 and 1957.
Since 11 of Elvis’ number ones were on various Billboard pop charts over a “rapid-fire span” of three years, three months and three weeks, all which happened prior to the Hot 100's Aug. 4, 1958 inception, he would not be on that particular list.
They said that prior to the Hot 100, Billboard printed various pop charts based either solely on airplay, sales or juke box plays. This includes the Top 100, which was a sales-based chart. Elvis’ number ones on those pre-1958 charts have been counted by some sources in conjunction with the Hot 100 when considered among number one songs in the rock ‘n’ roll era.
So Billboard is in no way changing their system to reflect less number ones for Elvis and they were very much wanting to make sure we let the fans know."
Personally, I still think it is a stupid decision by Billboard and will no doubt create the wrong impression with many of their readers and lead to the situation where such statistics will be quoted in musical journals throughout the world.
Source; EPE – Billboard – Brian Quinn / EpGold