Well, as a marketing professional, I get it. Your logo is your most recognizable aspect of your brand; it should be consistent, and identical, on everything you do. If the white on red rectangle is the "official" Marvel logo, then it should be used, on everything, from your movie credits to toys to corporate stationary to your book spines. It's just marketing 101.

However, I think an exception could have been made to "grandfather in" on existing lines like the Masterworks, or to finish off existing runs (like the Hickman FF example) and start the new branding with the next run. Marvel Now would have been a great time to start the new look, instead of in the middle of some runs!