Our project is a factory with historically a 95% male workforce. The restroom design accounts for this. Can I argue that the male/female gender ratio is different than 50/50?

GBCI provides very little leeway for non-standard gender ratios, even in a case just like you describe. Even a 10% bump toward women to account for possible future trends was not deemed sufficient. GBCI is only granting exceptions if a nonstandard gender ratio can be verified for the lifespan of the building.