Yes, that was another similar Jeep. You can also see dark brown Jeep Wagoneers in 'Witness for the Persecution' and 'And in This Corner, Luke Duke'. In the latter, you actually get to see the Wagoneer badge close-up when Luke is being kidnapped, which is unusual product placement for the show.
From season 3, the end credits included "Some vehicles supplied by AMC". They owned Jeep at the time, so the Wagoneers were probably just supplied to promote the model. I've spotted a few differences: there were at least three different wheel designs, there are two different shapes for the wood trim on the sides, and at least one of them had a chrome bull guard, so I'm now doubting that it was the same vehicle. It's just strange that they were always the same color when they were driven by different characters, so there was no need for continuity.