They're just the wear indicators as I've found out, needed but completely unrelated. I'm starting to think that the warmer discs may be a problem but at the same time a red herring. Everything is seated properly, the brakes clamp and there's no vibration through the pedals at all or any sound of grinding/pulsation when rotating the rear wheels.
I'm getting it up again to check the front driveshafts, but I think spinning them in the air won't reveal much but I can feel the pulsation through the footrest. I even checked the rotation rates vs the pulsation interval, it directly corresponds with the wheel speed so it narrows it down to;
- Still brakes but the front ones instead (ignoring the hot rear disc)
- Dodgy tyres
- Front driveshafts
- Anything else that rotates at wheel speed
If it was truly brakes they would eventually not pulsate as the pad material would wear off, leaving a nice gap and killing the noise, the fact it went away after doing the front brakes suggests that something they did during replacement or MOT temporarily fixed the issue, perhaps simply unloading the wheel for a length of time let the tyre regain its shape. But at the moment i'm clutching at straws and considering throwing in the towel on it.