Those are issues with the affiliate league, not the Academy.
The Girls Academy will face an entirely different set of issues. The primary goal of HS girls soccer players is to leverage it into college admissions and scholarships, not the dream of playing professionally. Many of the girls clubs have incredible college contact networks developed over many years. That will be hard to duplicate for NYCFC and will keep many top girls away.
The girls academy team are not likely to be up to part with the boys because of this.
Kids will go where the instruction is best. Your point is well taken regarding college connections.