Just FYI, I'm not sure how accurate that is based on your "sources", because that goes right into Blue Bayou. Which I'm 100% sure Disney wouldn't be getting rid of for an indoor queue as its the only major upscale table service restaurant Disneyland proper has.
So that means to me, especially if Pieces of Eight is staying, that its only the front corner of the building closest to the ride entrance up to the Royal Courtyard, ie Royal Veranda QSR and the Port Royal Curios and Curiosities shop, that would be used for this indoor queue. And that would make sense given that all the HM merch will go to the new HM giftshop and Pieces of Eight will be exclusive to Pirates merch, as mentioned before. So its not as large of a change as you originally made it seem.
I'm still not a fan overall though.