An MD-80 will not flex in and out 4 to 6 inches on each sidewall. In turbulence, there will be some modest twisting of the fuselage structure, and flexing fore and aft, which is particularly noticable when seated in the rear of the cabin and looking forward. It's seen most readily in the form of movement in the overhead bins. Perhaps some of the movement you described between the armrest and sidewall was lateral loading of the seat assembly moving toward the sidewall, or alternatively away from the sidewall.