Are you doing a geometry optimization? If you set symmetry to c1 and just are doing escf to get the TDMS, then the coordinates shouldn't shift.
Also, you're just comparing the TDMs correct? The origin of the TDM doesn't matter, as it's just a vector of the change in state densities (naively), so you can just compare the two vectors themselves.
For example, the angle between the x and y axis is 90 degrees. Similarly the angle between [10, 0, 0] and [0, 20, 0] is still 90 degrees. Origin shouldn't matter.
You are correct to be concerned with the possibility of rotation though, but your frame of reference in for the TDM shouldn't change if you're not doing a geometry optimization and you leave symmetry off.