Without a structural redesign, the use of the more flexible filaments will always be problematic for the Flux. The Bowen tube design means that the knurled wheel is pushing the filament down the tube, and every time the filament hits the side of the tube, it drags a little bit, making the filament behind the contact point flex a little, possibly hitting the other side of the tube and adding more friction. With enough contact points, the friction of the filament in the tube increases to the point where the knurled wheel can't push the filament down the tube. Think about trying to push a string through a straw.
A filament drive mounted directly on top of the print head doesn't have this problem, because it's only pushing the filament directly into the hot end, and is pulling the filament through the feed tube, making it straighten out. But putting the drive on the print head adds weight, imposing additional constraints on the movement of the print head and power delivery. It's possible that the Flux developers could design a filament drive that mounts on the top of the print head, but it would need both power (fed through the existing cable and out the bottom into the printhead) and control (no existing connections, so a new top end would need to be designed to feed control from the existing control board).