I have a custom buggy that I have raced at several GNCC events. No one ever said anything about it or that I couldn't race it. I just make sure it meets all the rules and then there is no hassle. I just sign up for the race as a Pilot.
That said, the best GNCC vehicle is a fully stock Pilot. It's the most reliable. Out of the 4 GNCC races I have entered, I have only finished 1, and that included a roll over on the last lap. The other 3 had buggy problems or mud issues resulting in problems that forced me to DNF. And I do race my buggy on short course tracks very successfully with a 2nd place overall finish this year. GNCC racing is extremely hard on vehicles.
Have you built a custom buggy before? I don't think it's possible to build a reliable, race ready vehicle for less cost than a Pilot. My buggy started as a rolling chassis complete with suspension and shocks that I got for close to nothing, and I used a snowmobile Engine, CVT, and chain case that also cost next to nothing. But for the money I now have into it I could have just bought a very nice Pilot with some mods plus a couple sets of wheels and tires.
This is me with my buggy on the left, and PilotGuy5 with his Pilot on the right.