Catalog sales alone account for the difference. Check the sales totals
per volume. Shingeki 1 - 11, limited edition versions of 12 and 13 sold a combined 4,902,793. Adding the standard editions of volume 12 and 13 equals 8,342,268 exactly. The Kuinaki Sentaku and Before the Fall do not appear to have been included in Shingeki's totals. One Piece had only one volume fully covered by this sales period, out of two total volumes released. Volume 72 came out seventeen days before the beginning of the chart period, missing the bulk of sales.
Volume 72 sold 2,354,005 copies during the two weeks before this chart period began. If both volumes were fully accounted for, One Piece would have sold 7,290,860 copies of two volumes.
Shingeki sold 8,342,268 copies of 13 volumes. Two volumes of One Piece sold 87% as many copies as thirteen volumes of Titan. Both new volumes of Titan were released during the sales period. Even without adding the number of copies One Piece volume 72 sold in the two weeks before the charts opened, One Piece sold 59% as many copies of 13 volumes of Shingeki with only one volume released during this sales period. Shingeki did not "win". It benefited from catalog sales and a lack of One Piece volumes. That's why total sales charts mean so little, they are just a matter of addition. Fewer volumes to add means lower sales. By volume tells a clearer story. One Piece retains a decisive edge there. Catalog sales were already beginning to decline when this chart period began. With a full compliment of volumes on sale by the end of the year, and declining catalog sales for Shingeki, One Piece should retake the lead when the full year charts are released in November. Comparing the popularity of two series, based only on sales, is, of course, extremely silly. Both series are massively popular in Japan. It's a big country, lots of things are popular. A heirarchy is not necessary, promoting no understanding. There really isn't a point trying to declare a winner. They are both winners.