I probably wouldn't give a wave to a stock JGC (I'd wave back if I received one, of course). For me, it's an Enthusiast thing.
Around my area, WK2s are aplenty, but modified rigs are hard to come by. But if I see a customized Jeep, I'd definitely give at least a nod to show my admiration and solidarity.
Unless they did a really tacky job of modifying. Then they get shunned.