It's a good question!
I think this because:
Rape (and sexual assault in general) are (usually) the result of a combination of power dynamics + sex. The other main assumption I'm making is that women are mostly sexually assaulted by men, and that men are sexually assaulted by both women and men in fairly equal numbers. (I think that women are as likely to be effed up in the head as men, but a substantial amount of male victims are victimized in male-only or default situations like the military or prison, and if all the people around you are men, all the assholes and rapists are too.)
So, examining each component separately:
Sex is going to be based on what sex acts are most common, and the most common male-female configurations focused on male pleasure have pain as a possibility for the female. Forcible vaginal penetration hurts more physically than being forced to penetrate, and being forced to gag on a penis is, in my opinion, more likely to cause pain than forced cunnilingus. So the acts themselves are more likely to cause physical pain.
With regard to power dynamics, I think most females are assaulted by men and those men are going to use their physical superiority more often (because it's the power tool they use). For male victims, I would guess whether or not their experience was physically painful would depend a lot on both the sex of their assaulter and how old they were at the time. I would expect boys that are victimized as children would be more likely to report physical pain since, like with adult women victims, there is often a physical strength differential between victim and assaulter. (Or, for example, I was physically abused by a woman as a child, and she was stronger than me.) I would also expect more physical pain from men who are sexually assaulted by other men in a social space where physical prowess is important.
The flip side of this is that I think men who are sexually assaulted by women are more likely to experience social and emotional pain/turmoil. Much like men are taught to wield their muscles as weapons, women are taught to wield our social abilities, and a woman who wants to humiliate a man or assert power over him is more likely to gaslight him, convince him to gaslight himself, etc. than beat the crap out of him. You also see this when some asshole women are dismissive of men getting erections during an assault. "He's hard, he wanted it."
I'd also hate to compare the experiences and I wouldn't say one is worse than the other. I think we should understand the variables that might cause differing results so that we can support all the victims. A focus on self-defense and overcoming feeling weak isn't going to help a male victim who could have physically stopped his attacker but didn't for social reasons: They need validation of their experiences and decisions. You know?