While only a certain number of rooms are released with any given discount - it's a certain number in their inventory. NOT physical rooms.
So to answer your question - yes. It doesn't matter if you have different rates, you'd still be eligible for connecting rooms.
However - as another poster mentioned, Disney guarantees connecting rooms only for groups with 2 adults and more children than will fit into a regular room. (ie: 2 adults and 3 kids traveling together at a value resort)
With the above exception, connecting (rooms with a door inside the room connecting the 2 of them) and adjoining (rooms next to each other, without a door inside) rooms are requests only.