He would do well in kickboxing for sure. He would have to adjust his stance and develop his skill set more, but I see no reason that he wouldn't do well in kickboxing. 3 rounds of 3 minutes is better for an athlete like him than 5x5 in MMA. He's got very good distance and timing (even Saenchai has said that).
Muay Thai would be a different kettle of fish altogether, not because muay thai is necessarily superior, but because of the clinch. That being said though, it's not like McGregor doesn't have an understanding of clinch from MMA - he'd likely adjust but I very much doubt he would be a strong muay thai fighter unless he lived the muay thai life training on a camp twice a day, 6 days a week.
Using McGregor's fighting style in MMA, to judge his potential efficiency in a different combat sport is misguided, because you wouldn't see him fight like that in kickboxing. He'd at least do decently, not because he's a savant (he isn't the best fighter in any of the weight divisions he's competed in) but because he's an explosive stand up fighter.