Yes you are right. Your values are overwritten in +network_generation/generated_network.m lines 91 – 101. Before calculating the region of interest (ROI), the positions of base stations are generated based on the intersite distance given as input parameter and based on the base station distribution. Then the ROI is calculated based on those base station positions.
You can solve this by adding the following code in the lines I mentioned above:
elseif LTE_config.manually_set_ROI == 1
roi_x = LTE_config.roi_x;
roi_y = LTE_config.roi_y;