From the wiki page, Generation Adidas is a joint venture between the MLS & USSF. The MLS is a male league, so that would explain to me why it doesn't apply to females. I thought the women's league is sponsored by Nike, so maybe Nike don't want to sponsor a project 40 for the women, which would be their prerogative. Have at it though.
WRT fully funded boys academies, they are not funded by USSF. USSF did subsidize DA & GDA, but disbanded both. If private entities (MLS teams & youth soccer clubs) want to provide fully funded boys academies, then that's on them. NWSL teams & youth soccer clubs could also fully fund girls academies if they want, but that would be on them.
AFAIK, US soccer pulled all money from youth sports. Have at it (again) though.
As to why clubs around the world run fully funded youth academies, I'd suggest that you google "Fifa solidarity payments". Clubs like Chelsea look to have self funding youth academies, rather than fully funded. The US, oddly, precluded themselves from solidarity payments - google the Crossfire case - but the MLS is now on board I believe. You might want to also look at how FC Dallas, for example, use (or used ...) their youth academy players to build their team and save money on their salary cap for MLS.