As someone who doesn't care if Bolden (Bebop and HoldenRye), happens or not, I see a couple of eyebrow-raising moments between the two within some of their games. There are a few blushy and awkward moments regarding the two that feel a bit out of "friend" territory in my opinion. If even I, a non-shipper for Bolden can have this opinion, then I see it perfectly reasonable that more romantic types or people who really love their relationship can see it as something more than just friendship.
Then again, the only perspective I have is what I've personally seen from the gays in my social circle and family/family friend relationships. But it's really impossible for this perspective to be altered without some sort of massive social experiment. It all boils down to personal experience, I don't notice many gay guy friend relationships around me that seem as intimate as Bebop removing all of Holden's violations for like eight seconds or Holden just happening to come back into the site when he hears Bebop is single again.
Just hasn't happened to come into notice to me, so I sense something more is going on. Every single one of us left "Guns and Hookers" feeling like something was up between the two.
Maybe for some people, Bolden's interactions are natural platonic behavior, due to experiencing such. It's hard to convince either side any differently, due to it all hinging on irreversible personal experiences.