Until that fix is released you can either downgrade SDL2 as mentioned there, or just force the mapping using SDL_GAMECONTROLLERCONFIG environment variable. Add this line to /etc/environment and then logout/login.
SDL_GAMECONTROLLERCONFIG=""050000005e040000e002000003090000,Xbox One Wireless Controller,a:b0,b:b1,back:b6,dpdown:h0.4,dpleft:h0.8,dpright:h0.2,dpup:h0.1,guide:b10,leftshoulder:b4,leftstick:b8,lefttrigger:a2,leftx:a0,lefty:a1,rightshoulder:b5,rightstick:b9,righttrigger:a5,rightx:a3,righty:a4,start:b7,x:b2,y:b3,","050000005e040000fd02000003090000,Xbox One Wireless Controller,a:b0,b:b1,back:b15,dpdown:h0.4,dpleft:h0.8,dpright:h0.2,dpup:h0.1,guide:b12,guide:b16,leftshoulder:b6,leftstick:b13,lefttrigger:a5,leftx:a0,lefty:a1,rightshoulder:b7,rightstick:b14,righttrigger:a4,rightx:a2,righty:a3,start:b11,x:b3,y:b4,""