The AFL doesn't govern SA and WA footy, but the VFA handed over to the AFL in about 1995.There was a stat a few years ago that kids drafted from SA spent more time on AFL lists, and played more games on average than kids from any other state. Not sure if that's still the case.
Point is that kids from Vic get preferenced in the draft over kids from SA and WA, when stats show they probably shouldn't.
Not to mention the amount of money the AFL puts into funding Vic talent, while doing SFA for SA. It's expected the SANFL and it's club do the lions share.
Now if the AFL was legit, it would make the VFL in charge of talent in Victoria. Let's see how the results of that got borne out.
So to part answer about the AFL fund for Vic talent, it is their job, they govern the league.