The factory placement is a "one-size-fits-all" WAG. While it can be a useful benchmark, you can do much better by adjusting the seat placement to suit your body (and your gear load).
Adjusting the kayak trim is an important ritual for many racers, and the seat on most race kayaks is on a microadjustable track to facilitate.
Brent Reitz provides some good ideas at http://www.wildsprint.com/site/index.php/resources/index-single/avoid_the_squat_how_to_trim_your_boat/.
The key is that you want dynamic trim (paddling at your normal speed), rather than static trim (sitting stationary).
Touring Kayak Paddles
Wall Mount Boat Racks
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