One small bug: note the functionality of "hiding/revealing" the waypoint/pinpoint (etc.) whenever you enter or exit a specific range. Initially, the UI elements indeed respect the transparency settings. However, when you approach those waypoints and they "hide", upon exiting range of those waypoints the transprency defaults back to 100% when they are revealed again. You can get back the desired transparency by heading into the WaypointUI config UI again and moving the opacity slider forward/backward - but this is lost again when entering/exiting range of a waypoint.
Changelog for 1.4.1 mentions this is fixed but it still seems to be an issue in 12.0.5 using 1.4.1