The thing about Bobby and Sam is that both of those were post-Claremont friendships so I wouldn't count that as Claremont writing her to get along more with the guys. In Claremont's run, I don't remember her ever being super close to Piotr, Alex, or even Kurt. A lot of the Kurt/Rogue stuff only came after they were confirmed as siblings. Claremont spent more time with these two together as friends/siblings in X-Men Forever than he ever did in his first X-Men run. Then her other male teammate was Longshot but that relationship was a romantic one.
I can see why she would be perceived as a tomboy and thus one of the guys, but I think as Claremont originally wrote her, she herself didn't lean more towards the male X-Men over the female X-Men. If she leaned more towards a certain type of X-Men, it was usually the ones who had slightly darker outlooks on life like Wolverine, Rachel, Magneto, and Storm after her mohawk rather than the more innocent ones like Colossus, Nightcrawler, and Kitty. Like the time when she and Rachel are flying by and see muggers attacking someone. They rescue the guy only to learn that he was being attacked because he was spraying anti-mutant rhetoric and both Rogue and Rachel admitted that had they known, they wouldn't have bothered to save him.
Another indication that she didn't necessarily feel more at home with the guys than the girls is the fact that on the Brotherhood, I don't recall her ever being close to Pyro or Avalanche or even Blob after he joined. They were closer to her age than Mystique or Destiny would be and one might assume she'd want to hang out with people who aren't her parents, but she never gravitates towards them either.