It's simply a marketing ploy IMO, that way they can release a "New Extended Cut" at some point to double dip.
The standard set contains all the deleted and extended scenes which make up the extended version in the special features, so not integrating them within the main feature is deliberate.

I tend to disagree about physical media dying, there definitely is an adjustment in respect to volume and delivery due to the various medias available, but there will always be physical media sources.
The apocalypse on vinyl & tapes was proclaimed when CD's & Digital Downloads became the rage, and now we have more vinyl in a Sunrise store than anything else (apart from Funko's anyway).

Warner Archive is aggressively expanding it's catalogue and re-releasing previously OOP products, It might not be worth the money for Warner as a corporation to invest into future physical media ventures, but there will always be someone ready to take it over. That's my five cents worth anyway......