For what it's worth, my humble opinion...
Yes, I think it would have made a big difference. The article brings forth several issues about the horses I was unaware of. However that being said, the poor condition of the teams and the weight and difficulty of the Gatlings surely would have slowed Custer down. Which would have been a good thing. Maybe he would have arrived on time instead of early and could have completed the mission as planned with the other two prongs. But he had his sights set on glory and the White House. In reality, he probably would have faced a court martial for disobeying orders.
Also, the article mentions Gatlings are primarily used as a defense weapon rather than an offensive weapon. What did the author think the Custer battlefield was? A circle of soldiers surrounded by an attacking force 10 x their size. Not to mention that once the battle got going in earnest, the troopers spent the majority of their time trying to pry headless brass casings out of their trapdoors as the high copper content brass tended to stay expanded in a hot barrel and the extractors ripped the bases off them leaving the brass stuck in the chamber. How is a soldier supposed to fight like that? The Gatlings, in such instance would have been a godsend and may well have turned the battle. And if Custer had simply waited for the others, it most likely would have closed the book on the plains Indian wars right then and there.