This is pure speculation, but when they were first released, folks with the black/smoked glass complained of problems viewing the juice holes. The reasonable decision would then have been to offer a clear replacement option to address the issue. But that would have created another supply problem. They planned and likely obtained x number of clear and x number of smoked (x being total run for the product). The only way to quickly supply the black finish customers would have been to pull from the clear inventory. That would have imbalanced stocks, so giving the SS purchasers the smoked balanced out the supply issue, and they could claim they did it to "give their customers more customization options". Or at least that's how I would have spun the change.
I can understand the above scenario and appreciate the difficulties of supply management. But I sill would have preferred clear glass replacements for both my Merlins, not just one.