Whether to file them off or not is a personal decision, which is why I stopped short of suggesting the OP does so.

While leaving them on and re-adjusting the QR each time does offer some of the benefit of QR such as not needing tools, it isn't as convenient as with the original design wherein the nut was tight enough to stay put and turn with the skewer.

If you do leave the lips on, and if the nut is thick enough, here's a way you can eat the your cake and have it too.

Trim the skewer so it ends short of the top of the nut by a few millimeters, being sure to have at least 6mm engaged (nut must be tall enough). Assemble the wheel onto the fork, adjust the skewer tension exactly where you want it and thread a small set screw in from the end until it makes contact.

Once you have everything the way you want it, locktite the set screw in place as a depth gauge, and from then on you'll have a quick reference to re-establish the setting every time you re-install the wheel.