It shouldn't require the pilot to work anything out or have to think too much about things. If cleared to a Flight Level, you do so on the standard pressure setting. If cleared to an altitude, you do so on the QNH given. Nice and simple.
The vertical position of your aircraft in relation to the Transition Layer, Transition Level, or whatever, is nice to know but since you are letting ATC provide the vertical separation, then trust them to provide you with a safe clearance based on the datum of their choice.
If you take the non standard 'danger' thing too far, where do you stop ?? Should we ban opposite direction levels, for example in the Upper Airspace and out on Oceanic tracks, thereby reducing capacity by a large amount ?? Or do we let professionals on both sides of the mike have trust in the overall system providing a safe and conflict free flight path, as we always have ?