Alright, so I double checked photoshop and both layers are at 100% opacity with a Normal blend mode @edmaul69. The opacity is definitly set to 1.0 in the retroarch settings and yes, I do have a viewport set to the size of the transparent area of the overlay @AndrewH:
video_fullscreen_x = 1920
video_fullscreen_y = 1080
custom_viewport_width = 1440
custom_viewport_height = 1080
custom_viewport_x = 240
custom_viewport_y = 0
aspect_ratio_index = 22
input_overlay = "/opt/retropie/configs/all/retroarch/overlay/tv-old/Nintendo.cfg"
input_overlay_enable = true
input_overlay_opacity = 1.000000
input_overlay_scale = 1.000000
video_smooth = "true"
video_scale_integer = "false"
video_shader_enable = "false"
video_font_size = "16"
video_message_pos_x = 0.17
video_message_pos_y = 0.06
@edmaul69, I'll try using two overlays but I have a feeling I'll either get none or it'll display only the first one that appears in the cfg file.