Withholding the doc makes me think they will double dip. Knowing they created one is a giveaway. Best case scenario is the extended cut wouldn't be ready for the first wave of releases so they are withholding the doc for the ultimate edition. It would be nice if they would be up front about this, like Lord of the Rings. The sad truth is that studios are backing away from home video because it peaked over a decade ago. That's why there are tons of extended cuts from that era that just added some deleted scenes back in without director participation. Sony in particular beat the extended cut to death until they genuinely devalued the concept. Fox today isn't the same Fox that allowed Scott to create a director's cut of Kingdom of Heaven, gave it a limited theatrical run, and released a four-disc DVD. It's a different marketplace and the studio is under different leadership.
A lot of it also had to do with Lauzirika. He knows what the fans want and gives them 110%. I rewatch his docs frequently and they are exquisite. But Fox and even Ridley seem disinclined to continue the practice. If they want to create a flagship home video release, they should get Lauzirika back and follow his advice to a T.
Rereading the old box office prediction thread makes me wonder if the sparse features on this disc is a reflection of the poor box office. Hardly anybody predicted it would perform this poorly. Most people expected it to make at least double the amount it ended up making. It's entirely possible that Fox lost money on Covenant. It might have been a financial decision not to throw good money after bad. We may have only gotten a commentary because they already recorded it.