I am sorry that there is confusion. My personal opinion is that 7-pin mini-DIN connectors are confusing. Unfortunately, multiple vendors have different pin numberings, and things are further confused as some vendors choose to preserve numberings across the M-F boundary, while some do not (they have 1 mate with 2, 3 with 4, and, 5 with 7). This is the case, in this tutorial.
The pin numbering in the OI manual is for the female connector in the Create. The pin numbering in the Create 2 Serial to 3.3V Logic document is for the male connector on a cable. On the cable end, we chose to keep the pin numbering convention of a wire-ended cable that we use in a lot of the tutorials, which is made by a vendor named Tensility (part number 10-00543). Unfortunately, their pin numbering is the mirror of that on the Create. (There is a note to this effect on the bottom of the second column on the first page -- "Note that the Tensility cable uses the opposite pin numbering convention as Roomba.")
If you use this cable, and follow the color scheme in the tutorial, you'll be in good shape (one more gotcha is that there are two black wires, one of which is connected to the shell. A multimeter will help you figure out which one).
If you are just pushing wires into the Create connector itself, without a connector, (which I do not recommend,) use the diagram in the OI manual; it is drawn as if you were looking down upon the female receptacle pins in the robot. Be aware that TX on the Create should go to RX on the Pi (with a level shift), and vice versa!