Surely you can just stick with an IAS limit because that will measure the Bernoulli's in the air no matter what your altitude.
Nope wrong there I am afraid. Putting slats or flaps out at high mach will turn the airflow from managable transonic to unmanagable transonic or even supersonic... thats why there is a mach limit. Nothing to do with number of bernoullis at high alt, all to do with the bernoullis bunching up, causing shock wave effects MASSIVELY varying the centre of pressure on the wing and thus invalidating any design criteria the slats/flaps were originally designed to.
High lift wings can have transonic (and also >M 1.0) flow at aircraft subsonic speeds as low as M0.5-0.6, as all those high lift devices do wonders to pressure differentials. In other words, the wing goes transonic WELL before the aircraft does.
As an aside, one of the big design problems for designers isnt only wing transonics, its the flow between nacelles. You put them too close together and you get a lovely convergen divergent duct to accelerate flow with... and nasty weak shocks that do wonders for engine mount fatigue.