I've had similar problems as the OP. Large hot spots and blisters on the balls of my feet wearing racing flats (Flyknit racer, Streak Lt, and Streak 6). Going through an assortment of socks, lacing techniques,and taping did nothing to help. I've since retired the Flyknit racer. The Streak 6 is now just a tempo shoe. I still race in the Lt, but only on the roads 5k and less. I wear vaporfly flyknits for longer races. They still feel kind of warm, but I don't think I'm getting the same forefoot strike I did with the others.
P.S. I've heard that better arch support can help alleviate hot spots too, but never tested it.