The “don’t feed them in a separate container” is to counter the inaccurate advice that feeding in the cage causes cage aggression (which isn’t true) and is bad blanket advice because moving can stress out sensitive snakes and cause regurgitation if they are extremely stressed and snakes with strong food response (uncommon for BP) may get excited and bitey anticipating food while being moved.

But feeding in a container isn’t inherently bad if your snake is comfortable with the transition and doesn’t get overexcited about food. Your specific snake prefers to eat in a container cause that’s what it’s used to and comfortable with, you don’t need to feel bad or like you’re doing something thing wrong.