To answer your first question, I would say that the provinces are not party to these agreements. However, the provinces are reflected in them to the extent that the priorities that the communities set for themselves have a lot to do with the provinces' ability to work with them, particularly as regards the supply of services. It may be a priority for the community to develop better service delivery capability with the provinces. That will be recognized in the agreement, but the parties to the agreements are not the provinces.
I'm going to answer your second question. Even though the agreements were created when Bill S-3 had just barely been drafted or was being developed, they embody a number of the principles of that bill, that is to say the new Part VII concerning the Canadian Heritage's duty to play its role of assisting the federal institutions in supporting the communities.