As the clinches were broken up quicker by the Ref Kovalev gassed quicker

Don't think so, kovalev was visibly doing a lot more in this fight, and obviously had the plan to fight in the clinches to keep ward from racking points with the pity pats, unlike the first fight which the gameplan consisted mainly of neutralization. Ref had nothing to do with it, kovalev simply worked more, and him trying to do work on the inside gave ward more room to hit him with better shots inside too.