The lips on the fork ends are the result of paranoia about legal liability on the part of the fork's maker, or simple laziness in using the same dropouts as they do for the rest of their production.
Since the dropout is a cast or forged aluminum part, you can file it as you would anything else without concern about the carbon part. Or you can shop for track nuts with smaller flanges. For my part, if I found nice track nuts that fit I might go that route, but most likely would file the dropout, as I have all my road forks.
BTW- there's no regulations on track bike forks, either by the CPSC which deems them "special purpose" and exempt, or by the UCI, which adopted their own "lips" rule as an interpretation of their general rule that raced bikes must be stock and available for sale to the general public. Since the bikes are sold with lips, they must be raced with them. By the same logic, since track bikes are sold without, none are required for competition.
Meanwhile, the popularity of SS fixies as street bikes raises a legal question. Is it still a track bike if it's sold for general street use? This may be why you have lips on a "track" fork.
__________________
FB
Chain-L site
An ounce of diagnosis is worth a pound of cure.
Just because I'm tired of arguing, doesn't mean you're right.
“One accurate measurement is worth a thousand expert opinions” - Adm Grace Murray Hopper - USN
WARNING, I'm from New York. Thin skinned people should maintain safe distance.