Men aren't really that much less flexible, men who train for flexibility, like most figure skaters do will be extremely flexible. On the other hand, side-by-side quads will be much more possible for a male-male team as quad jumps aren't really possible for adult women. Quad jumps in women's skating are done by teenagers, who are starved and likely on puberty blockers to prevent them from reaching women's natural adult body weight levels. Currently, quad jumps aren't encouraged in pairs skating like they are in singles, as the additional points for the fourth rotation in pairs are minimal. But for two men s-b-s quads, won't be too much of a risk to aim for, so there are points available to a male-male team that aren't available to a male-female team.

The potential loss that a male-male team may suffer is in lifts, throwing and catching. It will be harder to lift the weight of a male partner. It may be harder to throw a male partner in thrown jumps, where the male skater throws the female in the air with enough force for her to execute multiple rotations. And it will almost certainly be harder to perform twists, ie where the male throws the female above his head in a horizontal position. She executes multiple rotations in the horizontal position and he catches her, still horizontal and then assists her in a perfect one foot, backwards landing. Throwing a male skater like that will be harder, it will be unlikely he could execute as many rotations from that throw. And if he could be thrown high enough for a triple rotation, catching him on landing would be incredibly difficult as the rotations increase the force of their weight.

But outside of ultra-endurance events, where women do appear to have a very real natural advantage, sports where women have an assumed advantage, like types of gymnastics, acrobatics, etc often turns out to not be true when men train to a high standard. So I wouldn't be at all surprised if it turned out that the male-male teams have no disadvantage and do have clear advantages. Also considering the not particularly beautiful Brian from Derry, who recently won a beauty contest, despite clearly not being even close to beautiful. I also wouldn't discount a male-male team from just being awarded extra points for artistry due to how stunning and brave they are.

And lastly, female pairs skaters struggle due to the fact that there are a lot more women who train for the sport than men. Women in this sport have incredible levels of competition and often end up competing below their natural level as they may not find a partner who can qualify for their level of competition. Getting a high level male partner, very often requires extensive bribery. Adding a bunch of men who weren't good enough to compete in male singles into the pool of women looking for a pairs partner, will worsen that.