Sounds like the law is designed to do an end run and limit truck modifications by regulating the rubber under the truck. If I understand correctly, you can't have a tire extending past the flare, and you can't run super-wide flares to cover the tire. Thankfully, this is a moment for you to carry on some West Virginia traditions: show some ingenuity and stick it to the man.
For inspection, swapping stock junk back on the Jeep is a common trick. But, it doesn't do anything to save you when some over zealous cop sees you riding your oversized tires the next day. My thought is this... you need to extend the body metal and then affix the flares. A body shop good with a welder ought to be able to hook you up. The front flares should be easy. The rear is gonna take some finesse to look right. The Full Size Jeeps have a nice built-in contoured metal flare... look online for some pics. Specifically a Cherokee Chief which had slightly more pronounced flares, if memory serves. If you could duplicate that look, or cut them off a junkyard FSJ and weld them on, then affix the 3" factory flares I think aesthetically you have something you can live with ... and you can stick it to the man!