I've done that as a way to stretch on a long slab ride. I've also sat on the passenger seat keeping my feet on the driver pegs. Easy trick when you're 6foot4.
But Sargent seat helped me a lot and I've done the Buel peg swap which lowered my feet a little extra. As I too suffer from knee issues, too much downhill skiing as a teenager, so my knees snap and crack like a campfire when I walk somedays. Just get off the bike every hour or so, even if it's just for 5mins. Do a quick little walk around the bike to help the blood flow and you'll be good to go again. If you wait utill you start to feel stiff it's too late and you'll fight it all day.