A last is basically the mould they use to make a shoe. It's surprisingly un-foot-shaped, but the upper is formed around the last (usually nailed to it) and then the sole is glued on after the upper material has taken it's shape (often by steaming it). As you say different shoes using different lasts can have very different shapes (one orthotic shoe company I know of has three different last shapes in 6 widths and 20-odd sizes each, and that's only for relatively normal-looking feet).
If your knee problem still persists (and even if it doesn't), try sitting with your legs hanging off the edge of a table (thighs parallel). Do your toes point out (particularly more on the right)? Now lie on your back and relax your legs. Are your toes still pointing in roughly the same direction (even more on the right, or the same as before)? If they point out further when you're on your back then you might have an in-built external hip rotation; nothing to worry about but it might explain the knee sticking out. Wedges won't help with this. And new (better) shoes won't either but they certainly won't do you any harm. Angling your cleats so your toes point inwards slightly might help push your knee back in, but be wary of knee ligament strain if you do.