You're certainly correct in identifying variability in germanium transistors as a known source of "good" vs "bad" pedals. And you are also correct in identifying the need to have a large sustainable supply of a givencomponent with given characteristics as crucial for a large company like EHX to keep a product in its line (the unavailability of the MN3005 delay chips for the Memory Man in the mid-80's almost shut down EHX). But it actually had nothing to do with germanium at all for the BMP. It has always used silicon bipolar transistors since the very first one. Indeed, EHX didn't really use ANY germanium in any of their products until quite recently. The issue - if we can call it an "issue", as opposed to natural variation - was the normally wide tolerances of capacitors, and not-quite-as-wide but still noticeable variation in silicon transistor gain. Caps play a strong role in the "sound" of Big Muffs, by shaping both the bottom and top end of the signal at a variety of strategic points in the circuit. Although biasing of silicon transistors can be adjusted to compensate and have precisely the same gain for each clipping stage for every single Big Muff coming off the line, and caps can be hand-selected to conform to some specified value, that entails labour costs that would increase the price of the pedal. EHX simply went with a circuit that worked, could be made for low cost, and it worked for every pedal coming off the line; just a little differently.
Variation in clipping diode forward voltage, variation in cap value, modest-but-influential tolerances in key resistors, and the aforementioned variation in transistors, all contribute to variation in the resulting sound.