As a controller, I would expect the pilot of any high-performance aircraft to be able to follow my instructions/requests. If the cleared level is an altitude, I would expect level reports etc to be QNH-based, if it's a FL, I would expect level to be referenced to 1013. If it's vital to be certain what setting is used I'll double check by asking the pilot (and use Mode C if it's available).
I'll do my best not to swap between the two settings (e.g. having cleared the pilot to a FL to then give a stop your climb at an altitude) but these things can and do happen for various reasons. If I have to do it I'll always give the QNH again if it's a stop at an altitude. Whilst it may be an inconvenience, pilots seem able to comply with instructions in these cases whatever altimeter setting procedures are used.
I've always got half a mind on vertical searation when I'm working around the Transition Layer and will build in a buffer to a clearance that will at least ensure a degree of vertical space if the wrong pressure is set.
No, it's not fail-safe and, no, it's not the perfect situation. And certainly building in a bit of extra vertical can't be done all the time (and probably never at some places). As a side issie, I kinda like the 10000ft or 18000ft Transition Alt idea but I'm wary of saying 'let's do it' without giving it a lot of thought to see what other problems might emerge because the rest of the UK's airspace and procedures are based on the lower levers.
My attitude may seem insular but reading this thread clearly shows the range of altimeter setting procedures that are used. Sitting on the ground, I'm not going to try and second guess what altimers are set at what pressure setting on any particular aircraft! If you're a pilot and feel happy that you could comply with the (sometimes messy) level instructions that a controller gives because you've always got altimeters set up to let you, this is good. If not, is it something to raise with your Ops?