The tire pressures in your owners manual is only applicable to the tire the bike came with. If you change brands, styles, or sizes then the pressures need to be adjusted for changes in construction and load ratings and how they relate to your riding style. Anymore the manufactures are suggesting higher pressure settings to prevent under inflation when riding 2 up. That is why they recommend the same pressures in the manual for 1 up or 2 up. They don't care about the tire wear so much as they care about litigation if a tire blows on a new bike from low air.
When in the business I saw more problems from people loading up the bike with accessories, gear and passenger and NOT adjusting the tire pressures for the added load. You most definately DO need to adjust your tire pressures to acount for the added weight of a passenger unless, You're already at a high pressure. Most manufacturers are now recommending pressures near or at the maximum tire pressures recommended on the sidewall of the tire. THAT is the holy grail. Do not excede it and do not run lower than 70 percent of it. And pay attention to the max load rating associated with that pressure on the sidewall. Most riders excede it unknowingly when packed to the gunnels and 2 up. If you need all that weight and it's more than the load rating of the 2 tires combined, you need to find higher load rated tires. If you do you'll find that the max pressure is often higher on the tires with higher load ratings. That's because the tire construction, load rating, and air pressure are all inter-dependant in providing safe opperation of the tire and long even wear.
In short yes! You should be running near or at the max air pressure on the sidewall when riding 2 up, and you need to run the suspension settings at least high enough to prevent bottoming and more if needed to improve ride quality and or handling.
I'm not shooting from the hip here I used to sell motorcycle tires for a living.