Can you send me a link to the journey planner results? There is no specific way to contribute improvements to the results, best way for now would be to leave feedback through the form in the title bar of the new website.
Edit: You also might get some mileage out of setting your walking speed to "Fast" and selecting "Routes with fewest changes"
Choosing 'fast walking' and 'routes with fewest changes' sort of worked, but it still shows a walking route which doesn't use the pedestrian-only bridge:
Even with the fast walking, they seem to have employed a slow walker to measure this. My walk to work I can do in 35 mins, which isn't at a terribly fast pace, but even TfL's fastest option reports it as taking 44mins http://www.tfl.gov.uk/plan-a-journey/results?IsAsync=true&Jp...
Edit: You also might get some mileage out of setting your walking speed to "Fast" and selecting "Routes with fewest changes"