The raphe is rather irregularly placed on the underside of the penis (from the foreskin all the way down the shaft and continuing onto the scrotum). So even if it seems off to the side or wavy, that's probably what it is. That seam is often slightly raised and colored, so if there's a bit of irritation in the diaper area, it can rub and get redder.
A slightly irritated raphe is my guess of what you're describing, and the line itself is nothing to worry about, just that there may be a little bit of skin irritation going on. Keep the area clean, change diapers frequently, exposure to air, and barrier cream when in diapers, also rule out other irritants like detergents or chemicals.
Gillian