Except that those two references are relating to vertical vents.
Page 9 in this one of the links addresses horizontal vents:
http://www.lennoxhearthproducts.com/...V-3328(II).pdf
See the table "Minimum Clearances Inches (millimeters)" on page 9, at "Vent" it shows 3" Top and 1" Sides and Bottom, the 3" Top has an "*" behind it which goes down to "
*Note: 3 in. (75 mm) above any horizontal/inclined vent component."