That is precisely what the coffee is for: apology, and mitigation of her own constantly and unintentionally negative presence in someone else's space. Even when somebody doesn't drink coffee, it's still a clear shorthand for a mea culpa that nearly everyone understands.

It's not a perfect solution, though-- and here's an example, in the form of someone who just had the shit scared out of them, who clearly does not appreciate being set on the back foot in their own space. Grace winces, apologetically. (Everything is apologetic.)

"Do you mean here as in right here, or in storage? Or on the ship? Or like, existentially?" Some of those answers are more difficult than others.