i have ultegra rx805 rear derailleur, same problem.. even with e-tube 3.4 i can only modify the point at which full sync shifts the front derailleur as a reACTION o shifting the rear derailleur.. to heavier downhill gearing and not the point (moving rear derailleur) to a more easier uphill gear, i too was struggling with the cross chaining at the 2nd cog rear big cog front (uphill) so the solution is different.
adjusting the front derailleur micro adjust settings seems to solve the rub...