Creaturely, I have two swift frames, one is an older Zootr with the smaller diameter tubing and the other is the newer one like you have with the larger diameter tubing that I built myself after buying a frameset.

You've noticed the small notch in the seatstay for chain clearance. My older frame doesn't have this but the newer one does. In spite of the notch my chain still rubbed on the seatstay in the highest gear like yours does. My Zootr rear wheel came with two thin shims (about 2mm each) that went between the axle and dropouts. These shims, or washers if you prefer, spaces the cassette away from the Seatstay and since there's one on each side of the axle the wheel remains centered in the dropouts. Did your rear wheel come with these shims and if so are they installed between the axle and inside of the dropouts?

I changed cranksets and when I did this the chainline changed just enough to eliminate the problem. I think the easiest way to solve the problem is too add some shims.