When a value for magnetic declination is provided to EMpower, this value is used to rotate the tensor that represent the site. Note that if you are borrowing magnetic data from another station, or if you are using a remote magnetic station, you will need to provide the correct declination value in those recordings as well, so the whole tensor (which is composed by the data of the different acquisition channels combined for the processed site) is correctly rotated to true North.
Therefore, the MT tensor components for each pair of horizontal magnetic channels used in such tensor will be rotated to the declination provided in the recording data from where that pair of magnetic channels came from.
As the MT tensor represents the whole site, once it is rotated, it will show the effect of such rotation in all calculations derived from the tensor, such as apparent resistivity, impedance and tipper. So all derived quantities are rotated at once, because they come from the same rotated tensor.