I only have two pairs. Brown and black. I bought a bottle of some black repair that's basically paint or dye, made to cover wear on dress shoes.
The worst is when someone steps back and stands on your shoes in heels. I've found buffing out scuffs isn't an issue, but scratches change the surface of the leather, so like you've experience, they're still visible after a good polish. Also remember that people's eyes are typically at least 5 feet away from your shoes. If it's shell cordovan, you can buy a shoebone that works wonderfully, I've seen it with my own eyes.
My black dress shoes were damn cheap. I have a solution, but you probably won't want to use it on those shoes. You still want to avoid creasing areas in the leather and re-hydrate the stripped area with oils once done. If you don't polish them religiously and want a like new toe you're best bet is to simply re-do the finish. I personally only did this for my parade shoes - never general duty shoes/boots.
You should be left with a still fairly dark but faded color on your shoes. As another person mentioned you can use a hot spoon IF these are well polished shoes - the spoon will help smooth over all the layers of polish you may have. I've tried polishing out the scratches but it makes no difference. Worst case scenario and they won't fix a sharpie can cover them up.