There's nothing to stop the federal government from setting conditions before it transfers funds.
Right now, Madam Joly is trying to negotiate a set of ententes that have principles in them, but why couldn't there be a requirement in the law or a mains libre that she doesn't give money when she doesn't know where it's going? I'm sure she would feel that that would empower her.
Right now she gives money and the provincial government is able to say that it concerns education: “It's nothing to do with you, and we'll decide”. They have some rights to do that, but they don't have rights to require you to transfer the money. You have some leverage in this negotiation to say, “You don't get the money unless we're happy”.