Funny because my '14 came with the foam door cup holders. They were apparently not standard on all models (not sure if they are now or not), and I didn't want them. I took them out and sold them to some guy online. On my current truck I actually use them, so never took them out. I can certainly see both sides of wanting or not wanting them.
Although, even if you don't want them, they dang well better be there when the truck is new if they're supposed to be. I understand the OP's concern. Although do we know if they're a standard feature in the Big Horn level 2 (BH2) or are they an optional feature available with BH2? I know some features aren't even an available option on other trims, so maybe BH2 has them "available" whereas a Tradesman doesn't, but not necessarily something that should have been there depending on options selected.